23133101585

Committed 16 Mar 2026 07:45AM UTC coverage: 15.984% (+0.2%) from 15.811%

Build # 23133101585

Build Type

Pull #402

github

Committed by

web-flow

Commit Message

Merge bd8288c47 into 39c6ac11c

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

Run Details

717 of 5509 branches covered (13.02%)

Branch coverage included in aggregate %.

1809 of 10294 relevant lines covered (17.57%)

2.39 hits per line

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17.86

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<>();

    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;

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

knowledgepixels / nanodash / 23133101585

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