28936601485

Committed 08 Jul 2026 10:43AM UTC coverage: 28.314% (+0.2%) from 28.115%

Build # 28936601485

Build Type

Pull #545

github

Committed by

web-flow

Commit Message

Merge 2842605b1 into 3cb376d20

Pull Request Pull Request #545: feat: identify templates by embedded IRIs with dual-mode parser

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src/main/java/com/knowledgepixels/nanodash/template/TemplateData.java

package com.knowledgepixels.nanodash.template;

import com.knowledgepixels.nanodash.ApiCache;
import com.knowledgepixels.nanodash.QueryApiAccess;
import com.knowledgepixels.nanodash.Utils;
import net.trustyuri.TrustyUriUtils;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Statement;
import org.nanopub.Nanopub;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.QueryRef;
import org.nanopub.vocabulary.NTEMPLATE;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

/**
 * Singleton class that manages templates data.
 */
public class TemplateData implements Serializable {

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

    private static TemplateData instance;

    /**
     * Refreshes the templates data by creating a new instance of TemplateData.
     */
    public static synchronized void refreshTemplates() {
        logger.info("Refreshing templates...");
        instance = new TemplateData();
    }

    /**
     * Ensures that the TemplateData instance is loaded.
     */
    public static synchronized void ensureLoaded() {
        if (instance == null) refreshTemplates();
    }

    /**
     * Gets the singleton instance of TemplateData.
     *
     * @return the TemplateData instance
     */
    public static TemplateData get() {
        ensureLoaded();
        return instance;
    }

    private List<ApiResponseEntry> assertionTemplates, provenanceTemplates, pubInfoTemplates;
    private ConcurrentMap<String, Template> templateMap;

    /**
     * Constructor to initialize the TemplateData instance.
     */
    public TemplateData() {
        assertionTemplates = new ArrayList<>();
        provenanceTemplates = new ArrayList<>();
        pubInfoTemplates = new ArrayList<>();
        templateMap = new ConcurrentHashMap<>();
        refreshTemplates(assertionTemplates, QueryApiAccess.GET_ASSERTION_TEMPLATES);
        refreshTemplates(provenanceTemplates, QueryApiAccess.GET_PROVENANCE_TEMPLATES);
        refreshTemplates(pubInfoTemplates, QueryApiAccess.GET_PUBINFO_TEMPLATES);
    }

    private void refreshTemplates(List<ApiResponseEntry> templates, String queryId) {
        ApiResponse templateEntries = ApiCache.retrieveResponseSync(new QueryRef(queryId), true);
        String previousId = null;
        logger.info("Loading templates...");
        for (ApiResponseEntry entry : templateEntries.getData()) {
            if ("true".equals(entry.get("unlisted"))) continue;
            if (!entry.get("np").equals(previousId)) {
                templates.add(entry);
            }
            previousId = entry.get("np");
        }
        templates.sort(templateComparator);
    }

    /**
     * Returns the list of assertion templates.
     *
     * @return a list of assertion templates
     */
    public List<ApiResponseEntry> getAssertionTemplates() {
        return assertionTemplates;
    }

    /**
     * Returns the list of provenance templates.
     *
     * @return a list of provenance templates
     */
    public List<ApiResponseEntry> getProvenanceTemplates() {
        return provenanceTemplates;
    }

    /**
     * Returns the list of publication information templates.
     *
     * @return a list of publication information templates
     */
    public List<ApiResponseEntry> getPubInfoTemplates() {
        return pubInfoTemplates;
    }

    /**
     * Returns a Template object for the given template ID. The ID may be either
     * form: the nanopublication URI, or (for templates with embedded identity) the
     * embedded template-node IRI.
     *
     * @param id the ID of the template
     * @return the Template object if found, or null if not found or invalid
     */
    public Template getTemplate(String id) {
        Template template = templateMap.get(id);
        if (template != null) return template;
        String npId = Utils.stripToNanopubId(id);
        template = templateMap.get(npId);
        if (template != null) {
            templateMap.put(id, template);
            return template;
        }
        if (TrustyUriUtils.isPotentialTrustyUri(npId)) {
            try {
                Template t = new Template(npId);
                templateMap.put(id, t);
                templateMap.put(npId, t);
                templateMap.put(t.getId(), t);
                return t;
            } catch (Exception ex) {
                logger.error("Exception: {}", ex.getMessage());
                return null;
            }
        }
        return null;
    }

    /**
     * Registers a template from a Nanopub object directly, without fetching it from the registry.
     * This is useful for previewing templates that have not yet been published.
     *
     * @param np the Nanopub containing the template definition
     * @return the Template object, or null if the nanopub is not a valid template
     */
    public Template registerTemplate(Nanopub np) {
        String id = np.getUri().stringValue();
        Template template = templateMap.get(id);
        if (template != null) return template;
        try {
            Template t = new Template(np);
            templateMap.put(id, t);
            templateMap.put(t.getId(), t);
            return t;
        } catch (Exception ex) {
            logger.error("Exception registering template from nanopub: {}", ex.getMessage());
            return null;
        }
    }

    /**
     * Resolves a template ID to the ID of the latest version of that template,
     * following the supersedes chain of the containing nanopublication. Accepts
     * either ID form (nanopublication URI or embedded template-node IRI) and
     * returns the latest version's canonical ID ({@link Template#getId()}) — so
     * even when there is no newer version, the given ID is normalized to canonical
     * form. Falls back to the given ID if the template cannot be loaded.
     *
     * @param templateId the ID of the template
     * @return the canonical ID of the latest version, or the given ID as fallback
     */
    public String getLatestTemplateId(String templateId) {
        String npId = Utils.stripToNanopubId(templateId);
        String latestNpId = QueryApiAccess.getLatestVersionId(npId);
        Template latest = getTemplate(latestNpId);
        if (latest != null) return latest.getId();
        return templateId;
    }

    /**
     * Returns a Template object for the template of the given Nanopub.
     *
     * @param np the Nanopub from which to extract the template
     * @return the Template object if found, or null if not found or invalid
     */
    public Template getTemplate(Nanopub np) {
        IRI templateId = getTemplateId(np);
        if (templateId == null) return null;
        return getTemplate(templateId.stringValue());
    }

    /**
     * Returns a Template object for the provenance template of the given Nanopub.
     *
     * @param np the Nanopub from which to extract the provenance template
     * @return the Template object if found, or null if not found or invalid
     */
    public Template getProvenanceTemplate(Nanopub np) {
        IRI templateId = getProvenanceTemplateId(np);
        if (templateId == null) return null;
        return getTemplate(templateId.stringValue());
    }

    /**
     * Returns a set of Template objects for the publication information templates of the given Nanopub.
     *
     * @param np the Nanopub from which to extract the publication information templates
     * @return a set of Template objects
     */
    public Set<Template> getPubinfoTemplates(Nanopub np) {
        Set<Template> templates = new HashSet<>();
        for (IRI id : getPubinfoTemplateIds(np)) {
            templates.add(getTemplate(id.stringValue()));
        }
        return templates;
    }

    /**
     * Returns the template ID of the given Nanopub.
     *
     * @param nanopub the Nanopub from which to extract the template ID
     * @return the IRI of the template ID, or null if not found
     */
    public IRI getTemplateId(Nanopub nanopub) {
        for (Statement st : nanopub.getPubinfo()) {
            if (!st.getSubject().equals(nanopub.getUri())) continue;
            if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_TEMPLATE)) continue;
            if (!(st.getObject() instanceof IRI)) continue;
            return (IRI) st.getObject();
        }
        return null;
    }

    /**
     * Returns the provenance template ID of the given Nanopub.
     *
     * @param nanopub the Nanopub from which to extract the provenance template ID
     * @return the IRI of the provenance template ID, or null if not found
     */
    public IRI getProvenanceTemplateId(Nanopub nanopub) {
        for (Statement st : nanopub.getPubinfo()) {
            if (!st.getSubject().equals(nanopub.getUri())) continue;
            if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_PROVENANCE_TEMPLATE)) continue;
            if (!(st.getObject() instanceof IRI)) continue;
            return (IRI) st.getObject();
        }
        return null;
    }

    /**
     * Returns the set of publication information template IDs for the given Nanopub.
     *
     * @param nanopub the Nanopub from which to extract the publication information template IDs
     * @return a set of IRI objects representing the publication information template IDs
     */
    public Set<IRI> getPubinfoTemplateIds(Nanopub nanopub) {
        Set<IRI> iriSet = new HashSet<>();
        for (Statement st : nanopub.getPubinfo()) {
            if (!st.getSubject().equals(nanopub.getUri())) continue;
            if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_PUBINFO_TEMPLATE)) continue;
            if (!(st.getObject() instanceof IRI)) continue;
            iriSet.add((IRI) st.getObject());
        }
        return iriSet;
    }

    /**
     * Returns a list of Template objects from the given ApiResponse.
     *
     * @param apiResponse the ApiResponse containing template entries
     * @return a list of Template objects
     */
    public static List<Template> getTemplateList(ApiResponse apiResponse) {
        List<Template> templates = new ArrayList<>();
        for (ApiResponseEntry e : apiResponse.getData()) {
            String templateNpId = e.get("template_np");
            if (templateNpId == null) templateNpId = e.get("np");
            templates.add(TemplateData.get().getTemplate(templateNpId));
        }
        return templates;
    }

    private static final TemplateComparator templateComparator = new TemplateComparator();

    private static class TemplateComparator implements Comparator<ApiResponseEntry>, Serializable {

        /**
         * Compares two Template objects based on their labels.
         *
         * @param o1 the first object to be compared.
         * @param o2 the second object to be compared.
         * @return a negative integer, zero, or a positive integer as the first argument is less than, equal to, or greater than the second.
         */
        @Override
        public int compare(ApiResponseEntry o1, ApiResponseEntry o2) {
            return o1.get("label").compareTo(o2.get("label"));
        }

    }

}

1	package com.knowledgepixels.nanodash.template;
2
3	import com.knowledgepixels.nanodash.ApiCache;
4	import com.knowledgepixels.nanodash.QueryApiAccess;
5	import com.knowledgepixels.nanodash.Utils;
6	import net.trustyuri.TrustyUriUtils;
7	import org.eclipse.rdf4j.model.IRI;
8	import org.eclipse.rdf4j.model.Statement;
9	import org.nanopub.Nanopub;
10	import org.nanopub.extra.services.ApiResponse;
11	import org.nanopub.extra.services.ApiResponseEntry;
12	import org.nanopub.extra.services.QueryRef;
13	import org.nanopub.vocabulary.NTEMPLATE;
14	import org.slf4j.Logger;
15	import org.slf4j.LoggerFactory;
16
17	import java.io.Serializable;
18	import java.util.*;
19	import java.util.concurrent.ConcurrentHashMap;
20	import java.util.concurrent.ConcurrentMap;
21
22	/**
23	* Singleton class that manages templates data.
24	*/
25	public class TemplateData implements Serializable {
26
27	private static final Logger logger = LoggerFactory.getLogger(TemplateData.class);	9✔
28
29	private static TemplateData instance;
30
31	/**
32	* Refreshes the templates data by creating a new instance of TemplateData.
33	*/
34	public static synchronized void refreshTemplates() {
35	logger.info("Refreshing templates...");	9✔
36	instance = new TemplateData();	12✔
37	}	3✔
38
39	/**
40	* Ensures that the TemplateData instance is loaded.
41	*/
42	public static synchronized void ensureLoaded() {
43	if (instance == null) refreshTemplates();	6!
44	}	3✔
45
46	/**
47	* Gets the singleton instance of TemplateData.
48	*
49	* @return the TemplateData instance
50	*/
51	public static TemplateData get() {
52	ensureLoaded();	3✔
53	return instance;	6✔
54	}
55
56	private List<ApiResponseEntry> assertionTemplates, provenanceTemplates, pubInfoTemplates;
57	private ConcurrentMap<String, Template> templateMap;
58
59	/**
60	* Constructor to initialize the TemplateData instance.
61	*/
62	public TemplateData() {	6✔
63	assertionTemplates = new ArrayList<>();	15✔
64	provenanceTemplates = new ArrayList<>();	15✔
65	pubInfoTemplates = new ArrayList<>();	15✔
66	templateMap = new ConcurrentHashMap<>();	15✔
67	refreshTemplates(assertionTemplates, QueryApiAccess.GET_ASSERTION_TEMPLATES);	15✔
68	refreshTemplates(provenanceTemplates, QueryApiAccess.GET_PROVENANCE_TEMPLATES);	15✔
69	refreshTemplates(pubInfoTemplates, QueryApiAccess.GET_PUBINFO_TEMPLATES);	15✔
70	}	3✔
71
72	private void refreshTemplates(List<ApiResponseEntry> templates, String queryId) {
73	ApiResponse templateEntries = ApiCache.retrieveResponseSync(new QueryRef(queryId), true);	21✔
74	String previousId = null;	6✔
75	logger.info("Loading templates...");	9✔
76	for (ApiResponseEntry entry : templateEntries.getData()) {	33✔
77	if ("true".equals(entry.get("unlisted"))) continue;	21✔
78	if (!entry.get("np").equals(previousId)) {	18✔
79	templates.add(entry);	12✔
80	}
81	previousId = entry.get("np");	12✔
82	}	3✔
83	templates.sort(templateComparator);	9✔
84	}	3✔
85
86	/**
87	* Returns the list of assertion templates.
88	*
89	* @return a list of assertion templates
90	*/
91	public List<ApiResponseEntry> getAssertionTemplates() {
92	return assertionTemplates;	×
93	}
94
95	/**
96	* Returns the list of provenance templates.
97	*
98	* @return a list of provenance templates
99	*/
100	public List<ApiResponseEntry> getProvenanceTemplates() {
101	return provenanceTemplates;	×
102	}
103
104	/**
105	* Returns the list of publication information templates.
106	*
107	* @return a list of publication information templates
108	*/
109	public List<ApiResponseEntry> getPubInfoTemplates() {
110	return pubInfoTemplates;	×
111	}
112
113	/**
114	* Returns a Template object for the given template ID. The ID may be either
115	* form: the nanopublication URI, or (for templates with embedded identity) the
116	* embedded template-node IRI.
117	*
118	* @param id the ID of the template
119	* @return the Template object if found, or null if not found or invalid
120	*/
121	public Template getTemplate(String id) {
122	Template template = templateMap.get(id);	18✔
123	if (template != null) return template;	12✔
124	String npId = Utils.stripToNanopubId(id);	9✔
125	template = templateMap.get(npId);	18✔
126	if (template != null) {	6!
127	templateMap.put(id, template);	×
128	return template;	×
129	}
130	if (TrustyUriUtils.isPotentialTrustyUri(npId)) {	9!
131	try {
132	Template t = new Template(npId);	15✔
133	templateMap.put(id, t);	18✔
134	templateMap.put(npId, t);	18✔
135	templateMap.put(t.getId(), t);	21✔
136	return t;	6✔
137	} catch (Exception ex) {	×
138	logger.error("Exception: {}", ex.getMessage());	×
139	return null;	×
140	}
141	}
142	return null;	×
143	}
144
145	/**
146	* Registers a template from a Nanopub object directly, without fetching it from the registry.
147	* This is useful for previewing templates that have not yet been published.
148	*
149	* @param np the Nanopub containing the template definition
150	* @return the Template object, or null if the nanopub is not a valid template
151	*/
152	public Template registerTemplate(Nanopub np) {
153	String id = np.getUri().stringValue();	12✔
154	Template template = templateMap.get(id);	18✔
155	if (template != null) return template;	6!
156	try {
157	Template t = new Template(np);	15✔
158	templateMap.put(id, t);	18✔
159	templateMap.put(t.getId(), t);	21✔
160	return t;	6✔
161	} catch (Exception ex) {	×
162	logger.error("Exception registering template from nanopub: {}", ex.getMessage());	×
163	return null;	×
164	}
165	}
166
167	/**
168	* Resolves a template ID to the ID of the latest version of that template,
169	* following the supersedes chain of the containing nanopublication. Accepts
170	* either ID form (nanopublication URI or embedded template-node IRI) and
171	* returns the latest version's canonical ID ({@link Template#getId()}) — so
172	* even when there is no newer version, the given ID is normalized to canonical
173	* form. Falls back to the given ID if the template cannot be loaded.
174	*
175	* @param templateId the ID of the template
176	* @return the canonical ID of the latest version, or the given ID as fallback
177	*/
178	public String getLatestTemplateId(String templateId) {
179	String npId = Utils.stripToNanopubId(templateId);	×
180	String latestNpId = QueryApiAccess.getLatestVersionId(npId);	×
181	Template latest = getTemplate(latestNpId);	×
182	if (latest != null) return latest.getId();	×
183	return templateId;	×
184	}
185
186	/**
187	* Returns a Template object for the template of the given Nanopub.
188	*
189	* @param np the Nanopub from which to extract the template
190	* @return the Template object if found, or null if not found or invalid
191	*/
192	public Template getTemplate(Nanopub np) {
193	IRI templateId = getTemplateId(np);	×
194	if (templateId == null) return null;	×
195	return getTemplate(templateId.stringValue());	×
196	}
197
198	/**
199	* Returns a Template object for the provenance template of the given Nanopub.
200	*
201	* @param np the Nanopub from which to extract the provenance template
202	* @return the Template object if found, or null if not found or invalid
203	*/
204	public Template getProvenanceTemplate(Nanopub np) {
205	IRI templateId = getProvenanceTemplateId(np);	×
206	if (templateId == null) return null;	×
207	return getTemplate(templateId.stringValue());	×
208	}
209
210	/**
211	* Returns a set of Template objects for the publication information templates of the given Nanopub.
212	*
213	* @param np the Nanopub from which to extract the publication information templates
214	* @return a set of Template objects
215	*/
216	public Set<Template> getPubinfoTemplates(Nanopub np) {
217	Set<Template> templates = new HashSet<>();	×
218	for (IRI id : getPubinfoTemplateIds(np)) {	×
219	templates.add(getTemplate(id.stringValue()));	×
220	}	×
221	return templates;	×
222	}
223
224	/**
225	* Returns the template ID of the given Nanopub.
226	*
227	* @param nanopub the Nanopub from which to extract the template ID
228	* @return the IRI of the template ID, or null if not found
229	*/
230	public IRI getTemplateId(Nanopub nanopub) {
231	for (Statement st : nanopub.getPubinfo()) {	×
232	if (!st.getSubject().equals(nanopub.getUri())) continue;	×
233	if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_TEMPLATE)) continue;	×
234	if (!(st.getObject() instanceof IRI)) continue;	×
235	return (IRI) st.getObject();	×
236	}
237	return null;	×
238	}
239
240	/**
241	* Returns the provenance template ID of the given Nanopub.
242	*
243	* @param nanopub the Nanopub from which to extract the provenance template ID
244	* @return the IRI of the provenance template ID, or null if not found
245	*/
246	public IRI getProvenanceTemplateId(Nanopub nanopub) {
247	for (Statement st : nanopub.getPubinfo()) {	×
248	if (!st.getSubject().equals(nanopub.getUri())) continue;	×
249	if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_PROVENANCE_TEMPLATE)) continue;	×
250	if (!(st.getObject() instanceof IRI)) continue;	×
251	return (IRI) st.getObject();	×
252	}
253	return null;	×
254	}
255
256	/**
257	* Returns the set of publication information template IDs for the given Nanopub.
258	*
259	* @param nanopub the Nanopub from which to extract the publication information template IDs
260	* @return a set of IRI objects representing the publication information template IDs
261	*/
262	public Set<IRI> getPubinfoTemplateIds(Nanopub nanopub) {
263	Set<IRI> iriSet = new HashSet<>();	×
264	for (Statement st : nanopub.getPubinfo()) {	×
265	if (!st.getSubject().equals(nanopub.getUri())) continue;	×
266	if (!st.getPredicate().equals(NTEMPLATE.WAS_CREATED_FROM_PUBINFO_TEMPLATE)) continue;	×
267	if (!(st.getObject() instanceof IRI)) continue;	×
268	iriSet.add((IRI) st.getObject());	×
269	}	×
270	return iriSet;	×
271	}
272
273	/**
274	* Returns a list of Template objects from the given ApiResponse.
275	*
276	* @param apiResponse the ApiResponse containing template entries
277	* @return a list of Template objects
278	*/
279	public static List<Template> getTemplateList(ApiResponse apiResponse) {
280	List<Template> templates = new ArrayList<>();	×
281	for (ApiResponseEntry e : apiResponse.getData()) {	×
282	String templateNpId = e.get("template_np");	×
283	if (templateNpId == null) templateNpId = e.get("np");	×
284	templates.add(TemplateData.get().getTemplate(templateNpId));	×
285	}	×
286	return templates;	×
287	}
288
289	private static final TemplateComparator templateComparator = new TemplateComparator();	15✔
290
291	private static class TemplateComparator implements Comparator<ApiResponseEntry>, Serializable {
292
293	/**
294	* Compares two Template objects based on their labels.
295	*
296	* @param o1 the first object to be compared.
297	* @param o2 the second object to be compared.
298	* @return a negative integer, zero, or a positive integer as the first argument is less than, equal to, or greater than the second.
299	*/
300	@Override
301	public int compare(ApiResponseEntry o1, ApiResponseEntry o2) {
302	return o1.get("label").compareTo(o2.get("label"));	24✔
303	}
304
305	}
306
307	}

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