23622439422

Committed 26 Mar 2026 11:05PM UTC coverage: 67.082% (-2.4%) from 69.473%

Build # 23622439422

Build Type

push

github

Committed by

tkuhn

Commit Message

feat: detect and recover from Nanopub Registry resets

When the registry is reset and repopulated, its load counter restarts
from 0 while nanopub-query's stored counter remains high, causing it
to silently serve stale data. This adds detection via the registry's
setupId (Nanopub-Registry-Setup-Id header) and counter decrease, then
re-streams all nanopubs while skipping duplicates via existing per-repo
dedup in NanopubLoader.

- Read setupId from HEAD response alongside existing counter/status
- Persist setupId in admin repo, restore on startup
- Add RESETTING state to StatusController for counter reset
- Trigger resync on setupId change or counter decrease
- Re-stream with dedup preserves existing data, only loads new nanopubs

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

Coverage Stats

227 of 372 branches covered (61.02%)

Branch coverage included in aggregate %.

635 of 913 relevant lines covered (69.55%)

10.39 hits per line

Source File
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80.57

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

package com.knowledgepixels.query;

import org.eclipse.rdf4j.common.transaction.IsolationLevels;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.nanopub.vocabulary.NPA;

import java.util.Objects;

/**
 * Class to control the load status of the database.
 */
public class StatusController {

    /**
     * The load states in which the database can be.
     */
    public enum State {
        /**
         * The service is launching.
         */
        LAUNCHING,
        /**
         * The service is loading.
         */
        LOADING_INITIAL,
        /**
         * The service is loading updates.
         */
        LOADING_UPDATES,
        /**
         * The service is ready to serve requests.
         */
        READY,
        /**
         * The service detected a registry reset and is about to resync.
         */
        RESETTING,
    }

    /**
     * Get the singleton instance of the StatusController.
     *
     * @return the StatusController instance
     */
    public static StatusController get() {
        return instance;
    }

    private final static StatusController instance = new StatusController();

    static final IRI HAS_REGISTRY_SETUP_ID =
            SimpleValueFactory.getInstance().createIRI(NPA.NAMESPACE, "hasRegistrySetupId");

    private boolean initialized = false;
    private State state = null;
    private long lastCommittedCounter = -1;
    private Long registrySetupId = null;
    private RepositoryConnection adminRepoConn;

    /**
     * Represents the current status of the service, including the load counter.
     */
    public static class LoadingStatus {

        /**
         * The current state of the service.
         */
        public final State state;

        /**
         * The current load counter.
         */
        public final long loadCounter;

        private LoadingStatus(State state, long loadCounter) {
            this.state = state;
            this.loadCounter = loadCounter;
        }

        /**
         * Create a new LoadingStatus instance.
         *
         * @param state       the current state of the service
         * @param loadCounter the current load counter
         * @return a new LoadingStatus instance
         */
        public static LoadingStatus of(State state, long loadCounter) {
            return new LoadingStatus(state, loadCounter);
        }

        @Override
        public boolean equals(Object o) {
            if (o == null || getClass() != o.getClass()) {
                return false;
            }
            LoadingStatus that = (LoadingStatus) o;
            return loadCounter == that.loadCounter && state == that.state;
        }

        @Override
        public int hashCode() {
            return Objects.hash(state, loadCounter);
        }

    }

    /**
     * Initialize the StatusController, fetching the last known state from the DB.
     * This must be called right after service startup, before loading any nanopubs.
     *
     * @return the current state and the last committed counter
     */
    public LoadingStatus initialize() {
        synchronized (this) {
            if (initialized) {
                throw new IllegalStateException("Already initialized");
            }
            state = State.LAUNCHING;
            adminRepoConn = TripleStore.get().getAdminRepoConnection();
            // Serializable, as the service state needs to be strictly consistent
            adminRepoConn.begin(IsolationLevels.SERIALIZABLE);
            // Fetch the state from the DB
            try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, NPA.HAS_STATUS, null, NPA.GRAPH)) {
                if (!statements.hasNext()) {
                    adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_STATUS, stateAsLiteral(state), NPA.GRAPH);
                } else {
                    var stateStatement = statements.next();
                    state = State.valueOf(stateStatement.getObject().stringValue());
                }
            }
            // Fetch the load counter from the DB
            try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, null, NPA.GRAPH)) {
                if (!statements.hasNext()) {
                    adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, adminRepoConn.getValueFactory().createLiteral(-1L), NPA.GRAPH);
                } else {
                    var counterStatement = statements.next();
                    var stringVal = counterStatement.getObject().stringValue();
                    lastCommittedCounter = Long.parseLong(stringVal);
                }
            }
            // Fetch the registry setup ID from the DB
            try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, null, NPA.GRAPH)) {
                if (statements.hasNext()) {
                    var setupIdStatement = statements.next();
                    registrySetupId = Long.parseLong(setupIdStatement.getObject().stringValue());
                }
                adminRepoConn.commit();
            } catch (Exception e) {
                if (adminRepoConn.isActive()) {
                    try {
                        adminRepoConn.rollback();
                    } catch (Exception rollbackException) {
                        // Transaction may not be registered on server (e.g., already committed, timed out, or connection reset)
                        // Log the rollback failure but don't mask the original exception
                    }
                }
                throw new RuntimeException(e);
            }
            initialized = true;
            return getState();
        }
    }

    /**
     * Get the current state of the service.
     *
     * @return the current state and the last committed counter
     */
    public LoadingStatus getState() {
        synchronized (this) {
            return LoadingStatus.of(state, lastCommittedCounter);
        }
    }

    /**
     * Transition the service to the LOADING_INITIAL state and update the load counter.
     * This should be called in two situations:
     * - By the main loading thread (after calling initialize()) to start loading the initial nanopubs.
     * - By the initial nanopub loader, as it processes the initial nanopubs.
     *
     * @param loadCounter the new load counter
     */
    public void setLoadingInitial(long loadCounter) {
        synchronized (this) {
            if (state != State.LAUNCHING && state != State.LOADING_INITIAL && state != State.RESETTING) {
                throw new IllegalStateException("Cannot transition to LOADING_INITIAL, as the " + "current state is " + state);
            }
            if (state != State.RESETTING && lastCommittedCounter > loadCounter) {
                throw new IllegalStateException("Cannot update the load counter from " + lastCommittedCounter + " to " + loadCounter);
            }
            updateState(State.LOADING_INITIAL, loadCounter);
        }
    }

    /**
     * Transition the service to the LOADING_UPDATES state and update the load counter.
     * This should be called by the updates loader, when it starts processing new nanopubs, or
     * when it finishes processing a batch of nanopubs.
     *
     * @param loadCounter the new load counter
     */
    public void setLoadingUpdates(long loadCounter) {
        synchronized (this) {
            if (state != State.LAUNCHING && state != State.LOADING_UPDATES && state != State.READY) {
                throw new IllegalStateException("Cannot transition to LOADING_UPDATES, as the " + "current state is " + state);
            }
            if (lastCommittedCounter > loadCounter) {
                throw new IllegalStateException("Cannot update the load counter from " + lastCommittedCounter + " to " + loadCounter);
            }
            updateState(State.LOADING_UPDATES, loadCounter);
        }
    }

    /**
     * Transition the service to the READY state.
     * This should be called by the loaders, after they finish their work.
     */
    public void setReady() {
        synchronized (this) {
            if (state != State.READY) {
                updateState(State.READY, lastCommittedCounter);
            }
        }
    }

    /**
     * Transition the service to the RESETTING state, resetting the load counter to -1.
     * This is triggered when a registry reset is detected (setupId changed or counter decreased).
     */
    public void setResetting() {
        synchronized (this) {
            if (state != State.READY && state != State.LOADING_UPDATES) {
                throw new IllegalStateException("Cannot transition to RESETTING, as the " + "current state is " + state);
            }
            updateState(State.RESETTING, -1);
        }
    }

    /**
     * Get the persisted registry setup ID.
     *
     * @return the registry setup ID, or null if not yet known
     */
    public Long getRegistrySetupId() {
        synchronized (this) {
            return registrySetupId;
        }
    }

    /**
     * Persist a new registry setup ID to the admin repo.
     *
     * @param setupId the new setup ID
     */
    public void setRegistrySetupId(long setupId) {
        synchronized (this) {
            try {
                adminRepoConn.begin(IsolationLevels.SERIALIZABLE);
                adminRepoConn.remove(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, null, NPA.GRAPH);
                adminRepoConn.add(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, adminRepoConn.getValueFactory().createLiteral(setupId), NPA.GRAPH);
                adminRepoConn.commit();
                registrySetupId = setupId;
            } catch (Exception e) {
                if (adminRepoConn.isActive()) {
                    try {
                        adminRepoConn.rollback();
                    } catch (Exception rollbackException) {
                        // Log the rollback failure but don't mask the original exception
                    }
                }
                throw new RuntimeException(e);
            }
        }
    }

    void updateState(State newState, long loadCounter) {
        synchronized (this) {
            try {
                // Serializable, as the service state needs to be strictly consistent
                adminRepoConn.begin(IsolationLevels.SERIALIZABLE);
                adminRepoConn.remove(NPA.THIS_REPO, NPA.HAS_STATUS, null, NPA.GRAPH);
                adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_STATUS, stateAsLiteral(newState), NPA.GRAPH);
                adminRepoConn.remove(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, null, NPA.GRAPH);
                adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, adminRepoConn.getValueFactory().createLiteral(loadCounter), NPA.GRAPH);
                adminRepoConn.commit();
                state = newState;
                lastCommittedCounter = loadCounter;
            } catch (Exception e) {
                if (adminRepoConn.isActive()) {
                    try {
                        adminRepoConn.rollback();
                    } catch (Exception rollbackException) {
                        // Transaction may not be registered on server (e.g., already committed, timed out, or connection reset)
                        // Log the rollback failure but don't mask the original exception
                    }
                }
                throw new RuntimeException(e);
            }
        }
    }

    private Literal stateAsLiteral(State s) {
        return adminRepoConn.getValueFactory().createLiteral(s.toString());
    }

    /**
     * Reset the StatusController for testing purposes.
     * This will clear the state and allow re-initialization.
     */
    void resetForTest() {
        synchronized (this) {
            initialized = false;
            state = null;
            lastCommittedCounter = -1;
            registrySetupId = null;
            adminRepoConn = null;
        }
    }

}

1	package com.knowledgepixels.query;
2
3	import org.eclipse.rdf4j.common.transaction.IsolationLevels;
4	import org.eclipse.rdf4j.model.IRI;
5	import org.eclipse.rdf4j.model.Literal;
6	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
7	import org.eclipse.rdf4j.repository.RepositoryConnection;
8	import org.nanopub.vocabulary.NPA;
9
10	import java.util.Objects;
11
12	/**
13	* Class to control the load status of the database.
14	*/
15	public class StatusController {	6✔
16
17	/**
18	* The load states in which the database can be.
19	*/
20	public enum State {	9✔
21	/**
22	* The service is launching.
23	*/
24	LAUNCHING,	18✔
25	/**
26	* The service is loading.
27	*/
28	LOADING_INITIAL,	18✔
29	/**
30	* The service is loading updates.
31	*/
32	LOADING_UPDATES,	18✔
33	/**
34	* The service is ready to serve requests.
35	*/
36	READY,	18✔
37	/**
38	* The service detected a registry reset and is about to resync.
39	*/
40	RESETTING,	18✔
41	}
42
43	/**
44	* Get the singleton instance of the StatusController.
45	*
46	* @return the StatusController instance
47	*/
48	public static StatusController get() {
49	return instance;	6✔
50	}
51
52	private final static StatusController instance = new StatusController();	12✔
53
54	static final IRI HAS_REGISTRY_SETUP_ID =	3✔
55	SimpleValueFactory.getInstance().createIRI(NPA.NAMESPACE, "hasRegistrySetupId");	15✔
56
57	private boolean initialized = false;	9✔
58	private State state = null;	9✔
59	private long lastCommittedCounter = -1;	9✔
60	private Long registrySetupId = null;	12✔
61	private RepositoryConnection adminRepoConn;
62
63	/**
64	* Represents the current status of the service, including the load counter.
65	*/
66	public static class LoadingStatus {
67
68	/**
69	* The current state of the service.
70	*/
71	public final State state;
72
73	/**
74	* The current load counter.
75	*/
76	public final long loadCounter;
77
78	private LoadingStatus(State state, long loadCounter) {	6✔
79	this.state = state;	9✔
80	this.loadCounter = loadCounter;	9✔
81	}	3✔
82
83	/**
84	* Create a new LoadingStatus instance.
85	*
86	* @param state the current state of the service
87	* @param loadCounter the current load counter
88	* @return a new LoadingStatus instance
89	*/
90	public static LoadingStatus of(State state, long loadCounter) {
91	return new LoadingStatus(state, loadCounter);	18✔
92	}
93
94	@Override
95	public boolean equals(Object o) {
96	if (o == null \|\| getClass() != o.getClass()) {	21✔
97	return false;	6✔
98	}
99	LoadingStatus that = (LoadingStatus) o;	9✔
100	return loadCounter == that.loadCounter && state == that.state;	45✔
101	}
102
103	@Override
104	public int hashCode() {
105	return Objects.hash(state, loadCounter);	45✔
106	}
107
108	}
109
110	/**
111	* Initialize the StatusController, fetching the last known state from the DB.
112	* This must be called right after service startup, before loading any nanopubs.
113	*
114	* @return the current state and the last committed counter
115	*/
116	public LoadingStatus initialize() {
117	synchronized (this) {	12✔
118	if (initialized) {	9✔
119	throw new IllegalStateException("Already initialized");	15✔
120	}
121	state = State.LAUNCHING;	9✔
122	adminRepoConn = TripleStore.get().getAdminRepoConnection();	12✔
123	// Serializable, as the service state needs to be strictly consistent
124	adminRepoConn.begin(IsolationLevels.SERIALIZABLE);	12✔
125	// Fetch the state from the DB
126	try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, NPA.HAS_STATUS, null, NPA.GRAPH)) {	39✔
127	if (!statements.hasNext()) {	9!
128	adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_STATUS, stateAsLiteral(state), NPA.GRAPH);	48✔
129	} else {
130	var stateStatement = statements.next();	×
131	state = State.valueOf(stateStatement.getObject().stringValue());	×
132	}
133	}
134	// Fetch the load counter from the DB
135	try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, null, NPA.GRAPH)) {	39✔
136	if (!statements.hasNext()) {	9!
137	adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, adminRepoConn.getValueFactory().createLiteral(-1L), NPA.GRAPH);	51✔
138	} else {
139	var counterStatement = statements.next();	×
140	var stringVal = counterStatement.getObject().stringValue();	×
141	lastCommittedCounter = Long.parseLong(stringVal);	×
142	}
143	}
144	// Fetch the registry setup ID from the DB
145	try (var statements = adminRepoConn.getStatements(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, null, NPA.GRAPH)) {	39✔
146	if (statements.hasNext()) {	9!
147	var setupIdStatement = statements.next();	×
148	registrySetupId = Long.parseLong(setupIdStatement.getObject().stringValue());	×
149	}
150	adminRepoConn.commit();	9✔
151	} catch (Exception e) {	×
152	if (adminRepoConn.isActive()) {	×
153	try {
154	adminRepoConn.rollback();	×
155	} catch (Exception rollbackException) {	×
156	// Transaction may not be registered on server (e.g., already committed, timed out, or connection reset)
157	// Log the rollback failure but don't mask the original exception
158	}	×
159	}
160	throw new RuntimeException(e);	×
161	}	3✔
162	initialized = true;	9✔
163	return getState();	15✔
164	}
165	}
166
167	/**
168	* Get the current state of the service.
169	*
170	* @return the current state and the last committed counter
171	*/
172	public LoadingStatus getState() {
173	synchronized (this) {	12✔
174	return LoadingStatus.of(state, lastCommittedCounter);	24✔
175	}
176	}
177
178	/**
179	* Transition the service to the LOADING_INITIAL state and update the load counter.
180	* This should be called in two situations:
181	* - By the main loading thread (after calling initialize()) to start loading the initial nanopubs.
182	* - By the initial nanopub loader, as it processes the initial nanopubs.
183	*
184	* @param loadCounter the new load counter
185	*/
186	public void setLoadingInitial(long loadCounter) {
187	synchronized (this) {	12✔
188	if (state != State.LAUNCHING && state != State.LOADING_INITIAL && state != State.RESETTING) {	36✔
189	throw new IllegalStateException("Cannot transition to LOADING_INITIAL, as the " + "current state is " + state);	24✔
190	}
191	if (state != State.RESETTING && lastCommittedCounter > loadCounter) {	27✔
192	throw new IllegalStateException("Cannot update the load counter from " + lastCommittedCounter + " to " + loadCounter);	24✔
193	}
194	updateState(State.LOADING_INITIAL, loadCounter);	12✔
195	}	9✔
196	}	3✔
197
198	/**
199	* Transition the service to the LOADING_UPDATES state and update the load counter.
200	* This should be called by the updates loader, when it starts processing new nanopubs, or
201	* when it finishes processing a batch of nanopubs.
202	*
203	* @param loadCounter the new load counter
204	*/
205	public void setLoadingUpdates(long loadCounter) {
206	synchronized (this) {	12✔
207	if (state != State.LAUNCHING && state != State.LOADING_UPDATES && state != State.READY) {	36✔
208	throw new IllegalStateException("Cannot transition to LOADING_UPDATES, as the " + "current state is " + state);	24✔
209	}
210	if (lastCommittedCounter > loadCounter) {	15✔
211	throw new IllegalStateException("Cannot update the load counter from " + lastCommittedCounter + " to " + loadCounter);	24✔
212	}
213	updateState(State.LOADING_UPDATES, loadCounter);	12✔
214	}	9✔
215	}	3✔
216
217	/**
218	* Transition the service to the READY state.
219	* This should be called by the loaders, after they finish their work.
220	*/
221	public void setReady() {
222	synchronized (this) {	12✔
223	if (state != State.READY) {	12✔
224	updateState(State.READY, lastCommittedCounter);	15✔
225	}
226	}	9✔
227	}	3✔
228
229	/**
230	* Transition the service to the RESETTING state, resetting the load counter to -1.
231	* This is triggered when a registry reset is detected (setupId changed or counter decreased).
232	*/
233	public void setResetting() {
234	synchronized (this) {	12✔
235	if (state != State.READY && state != State.LOADING_UPDATES) {	24✔
236	throw new IllegalStateException("Cannot transition to RESETTING, as the " + "current state is " + state);	24✔
237	}
238	updateState(State.RESETTING, -1);	12✔
239	}	9✔
240	}	3✔
241
242	/**
243	* Get the persisted registry setup ID.
244	*
245	* @return the registry setup ID, or null if not yet known
246	*/
247	public Long getRegistrySetupId() {
248	synchronized (this) {	12✔
249	return registrySetupId;	15✔
250	}
251	}
252
253	/**
254	* Persist a new registry setup ID to the admin repo.
255	*
256	* @param setupId the new setup ID
257	*/
258	public void setRegistrySetupId(long setupId) {
259	synchronized (this) {	12✔
260	try {
261	adminRepoConn.begin(IsolationLevels.SERIALIZABLE);	12✔
262	adminRepoConn.remove(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, null, NPA.GRAPH);	36✔
263	adminRepoConn.add(NPA.THIS_REPO, HAS_REGISTRY_SETUP_ID, adminRepoConn.getValueFactory().createLiteral(setupId), NPA.GRAPH);	48✔
264	adminRepoConn.commit();	9✔
265	registrySetupId = setupId;	12✔
266	} catch (Exception e) {	×
267	if (adminRepoConn.isActive()) {	×
268	try {
269	adminRepoConn.rollback();	×
270	} catch (Exception rollbackException) {	×
271	// Log the rollback failure but don't mask the original exception
272	}	×
273	}
274	throw new RuntimeException(e);	×
275	}	3✔
276	}	9✔
277	}	3✔
278
279	void updateState(State newState, long loadCounter) {
280	synchronized (this) {	12✔
281	try {
282	// Serializable, as the service state needs to be strictly consistent
283	adminRepoConn.begin(IsolationLevels.SERIALIZABLE);	12✔
284	adminRepoConn.remove(NPA.THIS_REPO, NPA.HAS_STATUS, null, NPA.GRAPH);	36✔
285	adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_STATUS, stateAsLiteral(newState), NPA.GRAPH);	42✔
286	adminRepoConn.remove(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, null, NPA.GRAPH);	36✔
287	adminRepoConn.add(NPA.THIS_REPO, NPA.HAS_REGISTRY_LOAD_COUNTER, adminRepoConn.getValueFactory().createLiteral(loadCounter), NPA.GRAPH);	48✔
288	adminRepoConn.commit();	9✔
289	state = newState;	9✔
290	lastCommittedCounter = loadCounter;	9✔
291	} catch (Exception e) {	×
292	if (adminRepoConn.isActive()) {	×
293	try {
294	adminRepoConn.rollback();	×
295	} catch (Exception rollbackException) {	×
296	// Transaction may not be registered on server (e.g., already committed, timed out, or connection reset)
297	// Log the rollback failure but don't mask the original exception
298	}	×
299	}
300	throw new RuntimeException(e);	×
301	}	3✔
302	}	9✔
303	}	3✔
304
305	private Literal stateAsLiteral(State s) {
306	return adminRepoConn.getValueFactory().createLiteral(s.toString());	21✔
307	}
308
309	/**
310	* Reset the StatusController for testing purposes.
311	* This will clear the state and allow re-initialization.
312	*/
313	void resetForTest() {
314	synchronized (this) {	12✔
315	initialized = false;	9✔
316	state = null;	9✔
317	lastCommittedCounter = -1;	9✔
318	registrySetupId = null;	9✔
319	adminRepoConn = null;	9✔
320	}	9✔
321	}	3✔
322
323	}

knowledgepixels / nanopub-query / 23622439422

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