20268226543

Committed 16 Dec 2025 12:39PM UTC coverage: 14.107% (-1.3%) from 15.358%

Build # 20268226543

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: replace VocabUtils with the ones defined in the nanopub-java library

Run Details

526 of 4946 branches covered (10.63%)

Branch coverage included in aggregate %.

1452 of 9075 relevant lines covered (16.0%)

2.11 hits per line

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0.0

src/main/java/com/knowledgepixels/nanodash/Project.java

package com.knowledgepixels.nanodash;

import com.knowledgepixels.nanodash.template.Template;
import com.knowledgepixels.nanodash.template.TemplateData;
import com.knowledgepixels.nanodash.vocabulary.KPXL_TERMS;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
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 java.io.Serializable;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;

import static com.knowledgepixels.nanodash.Utils.vf;

/**
 * Class representing a Nanodash project.
 */
public class Project implements Serializable {

    private static List<Project> projectList = null;
    private static ConcurrentMap<String, Project> projectsByCoreInfo = new ConcurrentHashMap<>();
    private static ConcurrentMap<String, Project> projectsById = new ConcurrentHashMap<>();

    /**
     * Refresh the list of projects from the given API response.
     *
     * @param resp The API response containing project data.
     */
    public static synchronized void refresh(ApiResponse resp) {
        projectList = new ArrayList<>();
        ConcurrentMap<String, Project> prevProjectsByCoreInfoPrev = projectsByCoreInfo;
        projectsByCoreInfo = new ConcurrentHashMap<>();
        projectsById.clear();
        for (ApiResponseEntry entry : resp.getData()) {
            Project project = new Project(entry.get("project"), entry.get("label"), entry.get("np"));
            Project prevProject = prevProjectsByCoreInfoPrev.get(project.getCoreInfoString());
            if (prevProject != null) project = prevProject;
            projectList.add(project);
            projectsByCoreInfo.put(project.getCoreInfoString(), project);
            projectsById.put(project.getId(), project);
        }
    }

    /**
     * Ensure that the project list is loaded. If not, it fetches the data from the API.
     */
    public static void ensureLoaded() {
        if (projectList == null) {
            refresh(QueryApiAccess.forcedGet(new QueryRef("get-projects")));
        }
    }

    /**
     * Get the list of all projects.
     */
    public static List<Project> getProjectList() {
        ensureLoaded();
        return projectList;
    }

    /**
     * Get a project by its ID.
     *
     * @param id The ID of the project.
     * @return The project with the given ID, or null if not found.
     */
    public static Project get(String id) {
        ensureLoaded();
        return projectsById.get(id);
    }

    /**
     * Mark all projects as needing data refresh.
     */
    public static void refresh() {
        ensureLoaded();
        for (Project project : projectList) {
            project.dataNeedsUpdate = true;
        }
    }

    private String id, label, rootNanopubId;
    private Nanopub rootNanopub = null;

    private String description = null;
    private List<IRI> owners = new ArrayList<>();
    private List<IRI> members = new ArrayList<>();
    private ConcurrentMap<String, IRI> ownerPubkeyMap = new ConcurrentHashMap<>();
    private List<Template> templates = new ArrayList<>();
    private Set<String> templateTags = new HashSet<>();
    private ConcurrentMap<String, List<Template>> templatesPerTag = new ConcurrentHashMap<>();
    private List<IRI> queryIds = new ArrayList<>();
    private IRI defaultProvenance = null;

    private boolean dataInitialized = false;
    private boolean dataNeedsUpdate = true;

    private Project(String id, String label, String rootNanopubId) {
        this.id = id;
        this.label = label;
        this.rootNanopubId = rootNanopubId;
        this.rootNanopub = Utils.getAsNanopub(rootNanopubId);

        for (Statement st : rootNanopub.getAssertion()) {
            if (st.getSubject().stringValue().equals(getId())) {
                if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {
                    description = st.getObject().stringValue();
                } else if (st.getPredicate().equals(KPXL_TERMS.HAS_OWNER) && st.getObject() instanceof IRI obj) {
                    addOwner(obj);
                } else if (st.getPredicate().equals(KPXL_TERMS.HAS_PINNED_TEMPLATE) && st.getObject() instanceof IRI obj) {
                    templates.add(TemplateData.get().getTemplate(obj.stringValue()));
                } else if (st.getPredicate().equals(KPXL_TERMS.HAS_PINNED_QUERY) && st.getObject() instanceof IRI obj) {
                    queryIds.add(obj);
                } else if (st.getPredicate().equals(NTEMPLATE.HAS_DEFAULT_PROVENANCE) && st.getObject() instanceof IRI obj) {
                    defaultProvenance = obj;
                }
            } else if (st.getPredicate().equals(NTEMPLATE.HAS_TAG) && st.getObject() instanceof Literal l) {
                templateTags.add(l.stringValue());
                List<Template> list = templatesPerTag.get(l.stringValue());
                if (list == null) {
                    list = new ArrayList<>();
                    templatesPerTag.put(l.stringValue(), list);
                }
                list.add(TemplateData.get().getTemplate(st.getSubject().stringValue()));
            }
        }

    }

    private void addOwner(IRI owner) {
        // TODO This isn't efficient for long owner lists:
        if (owners.contains(owner)) return;
        owners.add(owner);
        UserData ud = User.getUserData();
        for (String pubkeyhash : ud.getPubkeyhashes(owner, true)) {
            ownerPubkeyMap.put(pubkeyhash, owner);
        }
    }

    /**
     * Get the ID of the project.
     *
     * @return The project ID.
     */
    public String getId() {
        return id;
    }

    /**
     * Get the root nanopublication ID of the project.
     *
     * @return The root nanopublication ID.
     */
    public String getRootNanopubId() {
        return rootNanopubId;
    }

    /**
     * Get a string containing the core information of the project (ID and root nanopub ID).
     *
     * @return A string with the project ID and root nanopub ID.
     */
    public String getCoreInfoString() {
        return id + " " + rootNanopubId;
    }

    /**
     * Get the root nanopublication of the project.
     *
     * @return The root nanopublication.
     */
    public Nanopub getRootNanopub() {
        return rootNanopub;
    }

    /**
     * Get the label of the project.
     *
     * @return The project label.
     */
    public String getLabel() {
        return label;
    }

    /**
     * Get the description of the project.
     *
     * @return The project description.
     */
    public String getDescription() {
        return description;
    }

    /**
     * Check if the project data has been initialized.
     *
     * @return True if the data is initialized, false otherwise.
     */
    public boolean isDataInitialized() {
        triggerDataUpdate();
        return dataInitialized;
    }

    /**
     * Get the list of owners of the project.
     *
     * @return A list of IRIs representing the owners.
     */
    public List<IRI> getOwners() {
        triggerDataUpdate();
        return owners;
    }

    /**
     * Get the list of members of the project.
     *
     * @return A list of IRIs representing the members.
     */
    public List<IRI> getMembers() {
        triggerDataUpdate();
        return members;
    }

    /**
     * Get the list of templates associated with the project.
     *
     * @return A list of templates.
     */
    public List<Template> getTemplates() {
        return templates;
    }

    /**
     * Get the set of template tags associated with the project.
     *
     * @return A set of template tags.
     */
    public Set<String> getTemplateTags() {
        return templateTags;
    }

    /**
     * Get a map of templates categorized by their tags.
     *
     * @return A concurrent map where keys are tags and values are lists of templates.
     */
    public ConcurrentMap<String, List<Template>> getTemplatesPerTag() {
        return templatesPerTag;
    }

    /**
     * Get the list of query IDs associated with the project.
     *
     * @return A list of IRIs representing the query IDs.
     */
    public List<IRI> getQueryIds() {
        return queryIds;
    }

    /**
     * Get the default provenance IRI for the project.
     *
     * @return The default provenance IRI.
     */
    public IRI getDefaultProvenance() {
        return defaultProvenance;
    }

    private synchronized void triggerDataUpdate() {
        if (dataNeedsUpdate) {
            new Thread(() -> {
                for (ApiResponseEntry r : QueryApiAccess.forcedGet(new QueryRef("get-owners", "unit", id)).getData()) {
                    String pubkeyhash = r.get("pubkeyhash");
                    if (ownerPubkeyMap.containsKey(pubkeyhash)) {
                        addOwner(Utils.vf.createIRI(r.get("owner")));
                    }
                }
                members = new ArrayList<>();
                for (ApiResponseEntry r : QueryApiAccess.forcedGet(new QueryRef("get-members", "unit", id)).getData()) {
                    IRI memberId = Utils.vf.createIRI(r.get("member"));
                    // TODO These checks are inefficient for long member lists:
                    if (owners.contains(memberId)) continue;
                    if (members.contains(memberId)) continue;
                    members.add(memberId);
                }
                owners.sort(User.getUserData().userComparator);
                members.sort(User.getUserData().userComparator);
                dataInitialized = true;
            }).start();
            dataNeedsUpdate = false;
        }
    }

}

1	package com.knowledgepixels.nanodash;
2
3	import com.knowledgepixels.nanodash.template.Template;
4	import com.knowledgepixels.nanodash.template.TemplateData;
5	import com.knowledgepixels.nanodash.vocabulary.KPXL_TERMS;
6	import org.eclipse.rdf4j.model.IRI;
7	import org.eclipse.rdf4j.model.Literal;
8	import org.eclipse.rdf4j.model.Statement;
9	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
10	import org.nanopub.Nanopub;
11	import org.nanopub.extra.services.ApiResponse;
12	import org.nanopub.extra.services.ApiResponseEntry;
13	import org.nanopub.extra.services.QueryRef;
14	import org.nanopub.vocabulary.NTEMPLATE;
15
16	import java.io.Serializable;
17	import java.util.ArrayList;
18	import java.util.HashSet;
19	import java.util.List;
20	import java.util.Set;
21	import java.util.concurrent.ConcurrentHashMap;
22	import java.util.concurrent.ConcurrentMap;
23
24	import static com.knowledgepixels.nanodash.Utils.vf;
25
26	/**
27	* Class representing a Nanodash project.
28	*/
29	public class Project implements Serializable {
30
31	private static List<Project> projectList = null;	×
32	private static ConcurrentMap<String, Project> projectsByCoreInfo = new ConcurrentHashMap<>();	×
33	private static ConcurrentMap<String, Project> projectsById = new ConcurrentHashMap<>();	×
34
35	/**
36	* Refresh the list of projects from the given API response.
37	*
38	* @param resp The API response containing project data.
39	*/
40	public static synchronized void refresh(ApiResponse resp) {
41	projectList = new ArrayList<>();	×
42	ConcurrentMap<String, Project> prevProjectsByCoreInfoPrev = projectsByCoreInfo;	×
43	projectsByCoreInfo = new ConcurrentHashMap<>();	×
44	projectsById.clear();	×
45	for (ApiResponseEntry entry : resp.getData()) {	×
46	Project project = new Project(entry.get("project"), entry.get("label"), entry.get("np"));	×
47	Project prevProject = prevProjectsByCoreInfoPrev.get(project.getCoreInfoString());	×
48	if (prevProject != null) project = prevProject;	×
49	projectList.add(project);	×
50	projectsByCoreInfo.put(project.getCoreInfoString(), project);	×
51	projectsById.put(project.getId(), project);	×
52	}	×
53	}	×
54
55	/**
56	* Ensure that the project list is loaded. If not, it fetches the data from the API.
57	*/
58	public static void ensureLoaded() {
59	if (projectList == null) {	×
60	refresh(QueryApiAccess.forcedGet(new QueryRef("get-projects")));	×
61	}
62	}	×
63
64	/**
65	* Get the list of all projects.
66	*/
67	public static List<Project> getProjectList() {
68	ensureLoaded();	×
69	return projectList;	×
70	}
71
72	/**
73	* Get a project by its ID.
74	*
75	* @param id The ID of the project.
76	* @return The project with the given ID, or null if not found.
77	*/
78	public static Project get(String id) {
79	ensureLoaded();	×
80	return projectsById.get(id);	×
81	}
82
83	/**
84	* Mark all projects as needing data refresh.
85	*/
86	public static void refresh() {
87	ensureLoaded();	×
88	for (Project project : projectList) {	×
89	project.dataNeedsUpdate = true;	×
90	}	×
91	}	×
92
93	private String id, label, rootNanopubId;
94	private Nanopub rootNanopub = null;	×
95
96	private String description = null;	×
97	private List<IRI> owners = new ArrayList<>();	×
98	private List<IRI> members = new ArrayList<>();	×
99	private ConcurrentMap<String, IRI> ownerPubkeyMap = new ConcurrentHashMap<>();	×
100	private List<Template> templates = new ArrayList<>();	×
101	private Set<String> templateTags = new HashSet<>();	×
102	private ConcurrentMap<String, List<Template>> templatesPerTag = new ConcurrentHashMap<>();	×
103	private List<IRI> queryIds = new ArrayList<>();	×
104	private IRI defaultProvenance = null;	×
105
106	private boolean dataInitialized = false;	×
107	private boolean dataNeedsUpdate = true;	×
108
109	private Project(String id, String label, String rootNanopubId) {	×
110	this.id = id;	×
111	this.label = label;	×
112	this.rootNanopubId = rootNanopubId;	×
113	this.rootNanopub = Utils.getAsNanopub(rootNanopubId);	×
114
115	for (Statement st : rootNanopub.getAssertion()) {	×
116	if (st.getSubject().stringValue().equals(getId())) {	×
117	if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {	×
118	description = st.getObject().stringValue();	×
119	} else if (st.getPredicate().equals(KPXL_TERMS.HAS_OWNER) && st.getObject() instanceof IRI obj) {	×
120	addOwner(obj);	×
121	} else if (st.getPredicate().equals(KPXL_TERMS.HAS_PINNED_TEMPLATE) && st.getObject() instanceof IRI obj) {	×
122	templates.add(TemplateData.get().getTemplate(obj.stringValue()));	×
123	} else if (st.getPredicate().equals(KPXL_TERMS.HAS_PINNED_QUERY) && st.getObject() instanceof IRI obj) {	×
124	queryIds.add(obj);	×
125	} else if (st.getPredicate().equals(NTEMPLATE.HAS_DEFAULT_PROVENANCE) && st.getObject() instanceof IRI obj) {	×
126	defaultProvenance = obj;	×
127	}
128	} else if (st.getPredicate().equals(NTEMPLATE.HAS_TAG) && st.getObject() instanceof Literal l) {	×
129	templateTags.add(l.stringValue());	×
130	List<Template> list = templatesPerTag.get(l.stringValue());	×
131	if (list == null) {	×
132	list = new ArrayList<>();	×
133	templatesPerTag.put(l.stringValue(), list);	×
134	}
135	list.add(TemplateData.get().getTemplate(st.getSubject().stringValue()));	×
136	}
137	}	×
138
139	}	×
140
141	private void addOwner(IRI owner) {
142	// TODO This isn't efficient for long owner lists:
143	if (owners.contains(owner)) return;	×
144	owners.add(owner);	×
145	UserData ud = User.getUserData();	×
146	for (String pubkeyhash : ud.getPubkeyhashes(owner, true)) {	×
147	ownerPubkeyMap.put(pubkeyhash, owner);	×
148	}	×
149	}	×
150
151	/**
152	* Get the ID of the project.
153	*
154	* @return The project ID.
155	*/
156	public String getId() {
157	return id;	×
158	}
159
160	/**
161	* Get the root nanopublication ID of the project.
162	*
163	* @return The root nanopublication ID.
164	*/
165	public String getRootNanopubId() {
166	return rootNanopubId;	×
167	}
168
169	/**
170	* Get a string containing the core information of the project (ID and root nanopub ID).
171	*
172	* @return A string with the project ID and root nanopub ID.
173	*/
174	public String getCoreInfoString() {
175	return id + " " + rootNanopubId;	×
176	}
177
178	/**
179	* Get the root nanopublication of the project.
180	*
181	* @return The root nanopublication.
182	*/
183	public Nanopub getRootNanopub() {
184	return rootNanopub;	×
185	}
186
187	/**
188	* Get the label of the project.
189	*
190	* @return The project label.
191	*/
192	public String getLabel() {
193	return label;	×
194	}
195
196	/**
197	* Get the description of the project.
198	*
199	* @return The project description.
200	*/
201	public String getDescription() {
202	return description;	×
203	}
204
205	/**
206	* Check if the project data has been initialized.
207	*
208	* @return True if the data is initialized, false otherwise.
209	*/
210	public boolean isDataInitialized() {
211	triggerDataUpdate();	×
212	return dataInitialized;	×
213	}
214
215	/**
216	* Get the list of owners of the project.
217	*
218	* @return A list of IRIs representing the owners.
219	*/
220	public List<IRI> getOwners() {
221	triggerDataUpdate();	×
222	return owners;	×
223	}
224
225	/**
226	* Get the list of members of the project.
227	*
228	* @return A list of IRIs representing the members.
229	*/
230	public List<IRI> getMembers() {
231	triggerDataUpdate();	×
232	return members;	×
233	}
234
235	/**
236	* Get the list of templates associated with the project.
237	*
238	* @return A list of templates.
239	*/
240	public List<Template> getTemplates() {
241	return templates;	×
242	}
243
244	/**
245	* Get the set of template tags associated with the project.
246	*
247	* @return A set of template tags.
248	*/
249	public Set<String> getTemplateTags() {
250	return templateTags;	×
251	}
252
253	/**
254	* Get a map of templates categorized by their tags.
255	*
256	* @return A concurrent map where keys are tags and values are lists of templates.
257	*/
258	public ConcurrentMap<String, List<Template>> getTemplatesPerTag() {
259	return templatesPerTag;	×
260	}
261
262	/**
263	* Get the list of query IDs associated with the project.
264	*
265	* @return A list of IRIs representing the query IDs.
266	*/
267	public List<IRI> getQueryIds() {
268	return queryIds;	×
269	}
270
271	/**
272	* Get the default provenance IRI for the project.
273	*
274	* @return The default provenance IRI.
275	*/
276	public IRI getDefaultProvenance() {
277	return defaultProvenance;	×
278	}
279
280	private synchronized void triggerDataUpdate() {
281	if (dataNeedsUpdate) {	×
282	new Thread(() -> {	×
283	for (ApiResponseEntry r : QueryApiAccess.forcedGet(new QueryRef("get-owners", "unit", id)).getData()) {	×
284	String pubkeyhash = r.get("pubkeyhash");	×
285	if (ownerPubkeyMap.containsKey(pubkeyhash)) {	×
286	addOwner(Utils.vf.createIRI(r.get("owner")));	×
287	}
288	}	×
289	members = new ArrayList<>();	×
290	for (ApiResponseEntry r : QueryApiAccess.forcedGet(new QueryRef("get-members", "unit", id)).getData()) {	×
291	IRI memberId = Utils.vf.createIRI(r.get("member"));	×
292	// TODO These checks are inefficient for long member lists:
293	if (owners.contains(memberId)) continue;	×
294	if (members.contains(memberId)) continue;	×
295	members.add(memberId);	×
296	}	×
297	owners.sort(User.getUserData().userComparator);	×
298	members.sort(User.getUserData().userComparator);	×
299	dataInitialized = true;	×
300	}).start();	×
301	dataNeedsUpdate = false;	×
302	}
303	}	×
304
305	}

knowledgepixels / nanodash / 20268226543

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