23133579782

Committed 16 Mar 2026 08:00AM UTC coverage: 15.975% (+0.2%) from 15.811%

Build # 23133579782

Build Type

Pull #402

github

Committed by

web-flow

Commit Message

Merge 2ffdda823 into 39c6ac11c

Pull Request Pull Request #402: Fix unbounded memory growth and resource exhaustion

Run Details

717 of 5521 branches covered (12.99%)

Branch coverage included in aggregate %.

1811 of 10304 relevant lines covered (17.58%)

2.39 hits per line

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17.32

src/main/java/com/knowledgepixels/nanodash/domain/AbstractResourceWithProfile.java

package com.knowledgepixels.nanodash.domain;

import com.knowledgepixels.nanodash.ApiCache;
import com.knowledgepixels.nanodash.NanodashThreadPool;
import com.knowledgepixels.nanodash.QueryApiAccess;
import com.knowledgepixels.nanodash.ViewDisplay;
import com.knowledgepixels.nanodash.repository.SpaceRepository;
import com.knowledgepixels.nanodash.vocabulary.KPXL_TERMS;
import org.eclipse.rdf4j.model.IRI;
import org.nanopub.Nanopub;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.QueryRef;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.Serializable;
import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.Future;

/**
 * Abstract class representing a resource with a profile in the Nanodash application.
 * This class provides common functionality for resources that have associated profiles, such as spaces and users.
 */
public abstract class AbstractResourceWithProfile implements Serializable, ResourceWithProfile {

    private static final Logger logger = LoggerFactory.getLogger(AbstractResourceWithProfile.class);

    private static final Map<Class<?>, Map<String, AbstractResourceWithProfile>> instances = new ConcurrentHashMap<>();

    protected static final long DATA_REFRESH_TTL_MS = 60_000;

    private final String id;
    private Space space;
    private ResourceWithProfile data = new ResourceWithProfile();
    private volatile boolean dataInitialized = false;
    private volatile boolean dataNeedsUpdate = true;
    private volatile Long runUpdateAfter = null;
    private volatile long lastDataUpdate = 0;

    /**
     * Inner class to hold the data associated with a resource, including its view displays.
     */
    protected static class ResourceWithProfile implements Serializable {
        List<ViewDisplay> viewDisplays = new ArrayList<>();
    }

    /**
     * Checks if a resource with the given unique identifier exists in the system.
     *
     * @param id the unique identifier of the resource
     * @return true if a resource with the given id exists, false otherwise
     */
    public static boolean isResourceWithProfile(String id) {
        return get(id) != null;
    }

    /**
     * Retrieves an instance of AbstractResourceWithProfile by its unique identifier.
     *
     * @param id the unique identifier of the resource
     * @return the AbstractResourceWithProfile instance associated with the given id, or null if no such instance exists
     */
    public static AbstractResourceWithProfile get(String id) {
        for (Map<String, AbstractResourceWithProfile> map : instances.values()) {
            if (map.containsKey(id)) {
                return map.get(id);
            }
        }
        return null;
    }

    /**
     * Constructor for AbstractResourceWithProfile.
     *
     * @param id the unique identifier for this resource
     */
    protected AbstractResourceWithProfile(String id) {
        this.id = id;
        instances.computeIfAbsent(getClass(), k -> new ConcurrentHashMap<>()).put(id, this);
    }

    /**
     * Removes an instance of AbstractResourceWithProfile from the instances map based on its type and unique identifier.
     *
     * @param type the class type of the resource to remove
     * @param id   the unique identifier of the resource to remove
     */
    protected static void removeInstance(Class<?> type, String id) {
        Map<String, AbstractResourceWithProfile> map = instances.get(type);
        if (map != null) {
            map.remove(id);
        }
    }

    /**
     * Retrieves all instances of AbstractResourceWithProfile of a specific type.
     *
     * @param type the class type of the resources to retrieve
     * @return a map of resource IDs to AbstractResourceWithProfile instances of the specified type, or an empty map if no instances exist for that type
     */
    protected static Map<String, AbstractResourceWithProfile> getInstances(Class<?> type) {
        return instances.getOrDefault(type, Collections.emptyMap());
    }

    /**
     * Initializes the space for this resource.
     *
     * @param space the space to associate with this resource
     */
    protected void initSpace(Space space) {
        this.space = space;
        logger.info("Initialized space {} for resource {}", space.getId(), id);
    }

    @Override
    public String getId() {
        return id;
    }

    @Override
    public synchronized Future<?> triggerDataUpdate() {
        if (!dataNeedsUpdate && dataInitialized && System.currentTimeMillis() - lastDataUpdate > DATA_REFRESH_TTL_MS) {
            dataNeedsUpdate = true;
            dataInitialized = false;
        }
        if (dataNeedsUpdate) {
            logger.info("Data needs update for resource {}, starting update thread", id);
            dataNeedsUpdate = false;
            return NanodashThreadPool.submit(() -> {
                try {
                    if (runUpdateAfter != null) {
                        while (System.currentTimeMillis() < runUpdateAfter) {
                            Thread.sleep(100);
                        }
                        runUpdateAfter = null;
                    }

                    ResourceWithProfile newData = new ResourceWithProfile();

                    for (ApiResponseEntry r : ApiCache.retrieveResponseSync(new QueryRef(QueryApiAccess.GET_VIEW_DISPLAYS, "resource", id), true).getData()) {
                        if (space != null && !space.isAdminPubkey(r.get("pubkey"))) {
                            continue;
                        }
                        try {
                            newData.viewDisplays.add(ViewDisplay.get(r.get("display")));
                        } catch (IllegalArgumentException ex) {
                            logger.error("Couldn't generate view display object", ex);
                        }
                    }
                    data = newData;
                    dataInitialized = true;
                    lastDataUpdate = System.currentTimeMillis();
                } catch (Exception ex) {
                    logger.error("Error while trying to update data for resource {}", id, ex);
                    dataNeedsUpdate = true;
                }
            });
        }
        return null;
    }

    /**
     * Forces a refresh of the resource data after a specified delay.
     *
     * @param waitMillis the delay in milliseconds before the data refresh is triggered
     */
    public void forceRefresh(long waitMillis) {
        logger.info("Forcing refresh of resource {} after {} ms", id, waitMillis);
        dataNeedsUpdate = true;
        dataInitialized = false;
        runUpdateAfter = System.currentTimeMillis() + waitMillis;
    }

    /**
     * Static method to force a refresh of the resource data for all instances of AbstractResourceWithProfile.
     */
    public static void refresh() {
        instances.values().forEach(map -> map.values().forEach(AbstractResourceWithProfile::setDataNeedsUpdate));
    }

    @Override
    public Long getRunUpdateAfter() {
        return runUpdateAfter;
    }

    @Override
    public Space getSpace() {
        return space;
    }

    @Override
    public abstract String getNanopubId();

    @Override
    public abstract Nanopub getNanopub();

    public abstract String getNamespace();

    @Override
    public void setDataNeedsUpdate() {
        dataNeedsUpdate = true;
    }

    @Override
    public boolean isDataInitialized() {
        triggerDataUpdate();
        return dataInitialized;
    }

    @Override
    public List<ViewDisplay> getViewDisplays() {
        logger.info("Getting view displays for resource {}", id);
        return data.viewDisplays;
    }

    @Override
    public List<ViewDisplay> getTopLevelViewDisplays() {
        return getViewDisplays(true, getId(), null);
    }

    @Override
    public List<ViewDisplay> getPartLevelViewDisplays(String resourceId, Set<IRI> classes) {
        return getViewDisplays(false, resourceId, classes);
    }

    private List<ViewDisplay> getViewDisplays(boolean toplevel, String resourceId, Set<IRI> classes) {
        triggerDataUpdate();
        List<ViewDisplay> viewDisplays = new ArrayList<>();
        Set<IRI> viewKinds = new HashSet<>();

        // Results are sorted by date (most recent first); only the most recent per view-kind is considered
        for (ViewDisplay vd : getViewDisplays()) {
            IRI kind = vd.getViewKindIri();
            if (kind != null) {
                if (viewKinds.contains(kind)) {
                    continue;
                }
                viewKinds.add(kind);
            }

            if (vd.hasType(KPXL_TERMS.DEACTIVATED_VIEW_DISPLAY)) {
                continue;
            }

            if (!toplevel && vd.hasType(KPXL_TERMS.TOP_LEVEL_VIEW_DISPLAY)) {
                // Deprecated
                // do nothing
            } else if (vd.appliesTo(resourceId, classes)) {
                viewDisplays.add(vd);
            } else if (toplevel && vd.hasType(KPXL_TERMS.TOP_LEVEL_VIEW_DISPLAY)) {
                // Deprecated
                viewDisplays.add(vd);
            }
        }

        Collections.sort(viewDisplays);
        return viewDisplays;
    }

    @Override
    public abstract String getLabel();

    @Override
    public String toString() {
        return id;
    }

    /**
     * Gets the chain of superspaces from the current space up to the root space.
     *
     * @return the list of superspaces from the given space to the root space
     */
    @Override
    public List<AbstractResourceWithProfile> getAllSuperSpacesUntilRoot() {
        List<AbstractResourceWithProfile> chain = new ArrayList<>();
        Set<String> visited = new HashSet<>();
        collectAncestors(space, chain, visited);
        Collections.reverse(chain);
        return chain;
    }

    private void collectAncestors(Space current, List<AbstractResourceWithProfile> chain, Set<String> visited) {
        if (current == null) {
            return;
        }
        List<Space> parents = SpaceRepository.get().findSuperspaces(current);
        if (parents == null || parents.isEmpty()) {
            return;
        }
        Space parent = parents.getFirst();
        if (parent == null) {
            return;
        }
        String pid = parent.getId();
        if (pid == null || !visited.add(pid)) {
            return;
        }
        chain.add(parent);
        collectAncestors(parent, chain, visited);
    }

    /**
     * Checks if any view display of this resource applies to the given element ID and set of classes by triggering a data update and checking each view display for applicability.
     *
     * @param elementId the ID of the element to check for applicability
     * @param classes   the set of classes to check for applicability
     * @return true if any view display of this resource applies to the given element ID and set of classes, false otherwise
     */
    public boolean appliesTo(String elementId, Set<IRI> classes) {
        triggerDataUpdate();
        for (ViewDisplay v : getViewDisplays()) {
            if (v.appliesTo(elementId, classes)) {
                return true;
            }
        }
        return false;
    }

}

1	package com.knowledgepixels.nanodash.domain;
2
3	import com.knowledgepixels.nanodash.ApiCache;
4	import com.knowledgepixels.nanodash.NanodashThreadPool;
5	import com.knowledgepixels.nanodash.QueryApiAccess;
6	import com.knowledgepixels.nanodash.ViewDisplay;
7	import com.knowledgepixels.nanodash.repository.SpaceRepository;
8	import com.knowledgepixels.nanodash.vocabulary.KPXL_TERMS;
9	import org.eclipse.rdf4j.model.IRI;
10	import org.nanopub.Nanopub;
11	import org.nanopub.extra.services.ApiResponseEntry;
12	import org.nanopub.extra.services.QueryRef;
13	import org.slf4j.Logger;
14	import org.slf4j.LoggerFactory;
15
16	import java.io.Serializable;
17	import java.util.*;
18	import java.util.concurrent.ConcurrentHashMap;
19	import java.util.concurrent.Future;
20
21	/**
22	* Abstract class representing a resource with a profile in the Nanodash application.
23	* This class provides common functionality for resources that have associated profiles, such as spaces and users.
24	*/
25	public abstract class AbstractResourceWithProfile implements Serializable, ResourceWithProfile {
26
27	private static final Logger logger = LoggerFactory.getLogger(AbstractResourceWithProfile.class);	9✔
28
29	private static final Map<Class<?>, Map<String, AbstractResourceWithProfile>> instances = new ConcurrentHashMap<>();	15✔
30
31	protected static final long DATA_REFRESH_TTL_MS = 60_000;
32
33	private final String id;
34	private Space space;
35	private ResourceWithProfile data = new ResourceWithProfile();	15✔
36	private volatile boolean dataInitialized = false;	9✔
37	private volatile boolean dataNeedsUpdate = true;	9✔
38	private volatile Long runUpdateAfter = null;	9✔
39	private volatile long lastDataUpdate = 0;	9✔
40
41	/**
42	* Inner class to hold the data associated with a resource, including its view displays.
43	*/
44	protected static class ResourceWithProfile implements Serializable {	6✔
45	List<ViewDisplay> viewDisplays = new ArrayList<>();	18✔
46	}
47
48	/**
49	* Checks if a resource with the given unique identifier exists in the system.
50	*
51	* @param id the unique identifier of the resource
52	* @return true if a resource with the given id exists, false otherwise
53	*/
54	public static boolean isResourceWithProfile(String id) {
55	return get(id) != null;	×
56	}
57
58	/**
59	* Retrieves an instance of AbstractResourceWithProfile by its unique identifier.
60	*
61	* @param id the unique identifier of the resource
62	* @return the AbstractResourceWithProfile instance associated with the given id, or null if no such instance exists
63	*/
64	public static AbstractResourceWithProfile get(String id) {
65	for (Map<String, AbstractResourceWithProfile> map : instances.values()) {	33✔
66	if (map.containsKey(id)) {	12✔
67	return map.get(id);	15✔
68	}
69	}	3✔
70	return null;	6✔
71	}
72
73	/**
74	* Constructor for AbstractResourceWithProfile.
75	*
76	* @param id the unique identifier for this resource
77	*/
78	protected AbstractResourceWithProfile(String id) {	6✔
79	this.id = id;	9✔
80	instances.computeIfAbsent(getClass(), k -> new ConcurrentHashMap<>()).put(id, this);	42✔
81	}	3✔
82
83	/**
84	* Removes an instance of AbstractResourceWithProfile from the instances map based on its type and unique identifier.
85	*
86	* @param type the class type of the resource to remove
87	* @param id the unique identifier of the resource to remove
88	*/
89	protected static void removeInstance(Class<?> type, String id) {
90	Map<String, AbstractResourceWithProfile> map = instances.get(type);	×
91	if (map != null) {	×
92	map.remove(id);	×
93	}
94	}	×
95
96	/**
97	* Retrieves all instances of AbstractResourceWithProfile of a specific type.
98	*
99	* @param type the class type of the resources to retrieve
100	* @return a map of resource IDs to AbstractResourceWithProfile instances of the specified type, or an empty map if no instances exist for that type
101	*/
102	protected static Map<String, AbstractResourceWithProfile> getInstances(Class<?> type) {
103	return instances.getOrDefault(type, Collections.emptyMap());	18✔
104	}
105
106	/**
107	* Initializes the space for this resource.
108	*
109	* @param space the space to associate with this resource
110	*/
111	protected void initSpace(Space space) {
112	this.space = space;	9✔
113	logger.info("Initialized space {} for resource {}", space.getId(), id);	21✔
114	}	3✔
115
116	@Override
117	public String getId() {
118	return id;	9✔
119	}
120
121	@Override
122	public synchronized Future<?> triggerDataUpdate() {
123	if (!dataNeedsUpdate && dataInitialized && System.currentTimeMillis() - lastDataUpdate > DATA_REFRESH_TTL_MS) {	×
124	dataNeedsUpdate = true;	×
125	dataInitialized = false;	×
126	}
127	if (dataNeedsUpdate) {	×
128	logger.info("Data needs update for resource {}, starting update thread", id);	×
129	dataNeedsUpdate = false;	×
130	return NanodashThreadPool.submit(() -> {	×
131	try {
132	if (runUpdateAfter != null) {	×
133	while (System.currentTimeMillis() < runUpdateAfter) {	×
134	Thread.sleep(100);	×
135	}
136	runUpdateAfter = null;	×
137	}
138
139	ResourceWithProfile newData = new ResourceWithProfile();	×
140
141	for (ApiResponseEntry r : ApiCache.retrieveResponseSync(new QueryRef(QueryApiAccess.GET_VIEW_DISPLAYS, "resource", id), true).getData()) {	×
142	if (space != null && !space.isAdminPubkey(r.get("pubkey"))) {	×
143	continue;	×
144	}
145	try {
146	newData.viewDisplays.add(ViewDisplay.get(r.get("display")));	×
147	} catch (IllegalArgumentException ex) {	×
148	logger.error("Couldn't generate view display object", ex);	×
149	}	×
150	}	×
151	data = newData;	×
152	dataInitialized = true;	×
153	lastDataUpdate = System.currentTimeMillis();	×
154	} catch (Exception ex) {	×
155	logger.error("Error while trying to update data for resource {}", id, ex);	×
156	dataNeedsUpdate = true;	×
157	}	×
158	});	×
159	}
160	return null;	×
161	}
162
163	/**
164	* Forces a refresh of the resource data after a specified delay.
165	*
166	* @param waitMillis the delay in milliseconds before the data refresh is triggered
167	*/
168	public void forceRefresh(long waitMillis) {
169	logger.info("Forcing refresh of resource {} after {} ms", id, waitMillis);	×
170	dataNeedsUpdate = true;	×
171	dataInitialized = false;	×
172	runUpdateAfter = System.currentTimeMillis() + waitMillis;	×
173	}	×
174
175	/**
176	* Static method to force a refresh of the resource data for all instances of AbstractResourceWithProfile.
177	*/
178	public static void refresh() {
179	instances.values().forEach(map -> map.values().forEach(AbstractResourceWithProfile::setDataNeedsUpdate));	12✔
180	}	3✔
181
182	@Override
183	public Long getRunUpdateAfter() {
184	return runUpdateAfter;	×
185	}
186
187	@Override
188	public Space getSpace() {
189	return space;	×
190	}
191
192	@Override
193	public abstract String getNanopubId();
194
195	@Override
196	public abstract Nanopub getNanopub();
197
198	public abstract String getNamespace();
199
200	@Override
201	public void setDataNeedsUpdate() {
202	dataNeedsUpdate = true;	9✔
203	}	3✔
204
205	@Override
206	public boolean isDataInitialized() {
207	triggerDataUpdate();	×
208	return dataInitialized;	×
209	}
210
211	@Override
212	public List<ViewDisplay> getViewDisplays() {
213	logger.info("Getting view displays for resource {}", id);	×
214	return data.viewDisplays;	×
215	}
216
217	@Override
218	public List<ViewDisplay> getTopLevelViewDisplays() {
219	return getViewDisplays(true, getId(), null);	×
220	}
221
222	@Override
223	public List<ViewDisplay> getPartLevelViewDisplays(String resourceId, Set<IRI> classes) {
224	return getViewDisplays(false, resourceId, classes);	×
225	}
226
227	private List<ViewDisplay> getViewDisplays(boolean toplevel, String resourceId, Set<IRI> classes) {
228	triggerDataUpdate();	×
229	List<ViewDisplay> viewDisplays = new ArrayList<>();	×
230	Set<IRI> viewKinds = new HashSet<>();	×
231
232	// Results are sorted by date (most recent first); only the most recent per view-kind is considered
233	for (ViewDisplay vd : getViewDisplays()) {	×
234	IRI kind = vd.getViewKindIri();	×
235	if (kind != null) {	×
236	if (viewKinds.contains(kind)) {	×
237	continue;	×
238	}
239	viewKinds.add(kind);	×
240	}
241
242	if (vd.hasType(KPXL_TERMS.DEACTIVATED_VIEW_DISPLAY)) {	×
243	continue;	×
244	}
245
246	if (!toplevel && vd.hasType(KPXL_TERMS.TOP_LEVEL_VIEW_DISPLAY)) {	×
247	// Deprecated
248	// do nothing
249	} else if (vd.appliesTo(resourceId, classes)) {	×
250	viewDisplays.add(vd);	×
251	} else if (toplevel && vd.hasType(KPXL_TERMS.TOP_LEVEL_VIEW_DISPLAY)) {	×
252	// Deprecated
253	viewDisplays.add(vd);	×
254	}
255	}	×
256
257	Collections.sort(viewDisplays);	×
258	return viewDisplays;	×
259	}
260
261	@Override
262	public abstract String getLabel();
263
264	@Override
265	public String toString() {
266	return id;	×
267	}
268
269	/**
270	* Gets the chain of superspaces from the current space up to the root space.
271	*
272	* @return the list of superspaces from the given space to the root space
273	*/
274	@Override
275	public List<AbstractResourceWithProfile> getAllSuperSpacesUntilRoot() {
276	List<AbstractResourceWithProfile> chain = new ArrayList<>();	×
277	Set<String> visited = new HashSet<>();	×
278	collectAncestors(space, chain, visited);	×
279	Collections.reverse(chain);	×
280	return chain;	×
281	}
282
283	private void collectAncestors(Space current, List<AbstractResourceWithProfile> chain, Set<String> visited) {
284	if (current == null) {	×
285	return;	×
286	}
287	List<Space> parents = SpaceRepository.get().findSuperspaces(current);	×
288	if (parents == null \|\| parents.isEmpty()) {	×
289	return;	×
290	}
291	Space parent = parents.getFirst();	×
292	if (parent == null) {	×
293	return;	×
294	}
295	String pid = parent.getId();	×
296	if (pid == null \|\| !visited.add(pid)) {	×
297	return;	×
298	}
299	chain.add(parent);	×
300	collectAncestors(parent, chain, visited);	×
301	}	×
302
303	/**
304	* Checks if any view display of this resource applies to the given element ID and set of classes by triggering a data update and checking each view display for applicability.
305	*
306	* @param elementId the ID of the element to check for applicability
307	* @param classes the set of classes to check for applicability
308	* @return true if any view display of this resource applies to the given element ID and set of classes, false otherwise
309	*/
310	public boolean appliesTo(String elementId, Set<IRI> classes) {
311	triggerDataUpdate();	×
312	for (ViewDisplay v : getViewDisplays()) {	×
313	if (v.appliesTo(elementId, classes)) {	×
314	return true;	×
315	}
316	}	×
317	return false;	×
318	}
319
320	}

knowledgepixels / nanodash / 23133579782

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