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

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526 of 4946 branches covered (10.63%)

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1452 of 9075 relevant lines covered (16.0%)

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33.54

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

package com.knowledgepixels.nanodash.template;

import com.knowledgepixels.nanodash.LocalUri;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.GuidedChoiceItem;
import com.knowledgepixels.nanodash.component.PublishForm.FillMode;
import org.eclipse.rdf4j.model.*;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.nanopub.Nanopub;
import org.nanopub.NanopubUtils;
import org.nanopub.vocabulary.NPX;
import org.nanopub.vocabulary.NTEMPLATE;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.List;
import java.util.Set;

/**
 * ValueFiller is a utility class that processes a Nanopub and fills a TemplateContext.
 */
public class ValueFiller {

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    private Nanopub fillNp;
    private FillMode fillMode;
    private List<Statement> unusedStatements = new ArrayList<>();
    private int initialSize;
    private boolean formMode;
    private static final Logger logger = LoggerFactory.getLogger(ValueFiller.class);

    /**
     * Constructor for ValueFiller.
     *
     * @param fillNp      the Nanopub to fill
     * @param contextType the type of context to fill
     * @param formMode    if true, the filler will adapt to form mode, filtering out certain statements
     */
    public ValueFiller(Nanopub fillNp, ContextType contextType, boolean formMode) {
        this(fillNp, contextType, formMode, null);
    }

    /**
     * Constructor for ValueFiller with specified fill mode.
     *
     * @param fillNp      the Nanopub to fill
     * @param contextType the type of context to fill
     * @param formMode    if true, the filler will adapt to form mode, filtering out certain statements
     * @param fillMode    the fill mode to use, can be null for default behavior
     */
    public ValueFiller(Nanopub fillNp, ContextType contextType, boolean formMode, FillMode fillMode) {
        this.fillNp = fillNp;
        this.formMode = formMode;
        this.fillMode = fillMode;
        Set<Statement> statements;
        if (contextType == ContextType.ASSERTION) {
            statements = fillNp.getAssertion();
        } else if (contextType == ContextType.PROVENANCE) {
            statements = fillNp.getProvenance();
        } else {
            statements = fillNp.getPubinfo();
        }
        for (Statement st : statements) {
            Statement stT = transform(st);
            if (stT != null) unusedStatements.add(stT);
        }
        unusedStatements.sort((st1, st2) -> {
            String st1s = st1.getSubject() + " " + st1.getPredicate() + " " + st1.getObject();
            String st2s = st2.getSubject() + " " + st2.getPredicate() + " " + st2.getObject();
            return st1s.compareTo(st2s);
        });
        initialSize = unusedStatements.size();
    }

    /**
     * Fills the TemplateContext with the unused statements.
     *
     * @param context the TemplateContext to fill
     */
    public void fill(TemplateContext context) {
        try {
            context.fill(unusedStatements);
        } catch (UnificationException ex) {
            logger.error("Could not fill template context", ex);
        }
    }

    /**
     * Checks if the Nanopub has any statements.
     *
     * @return true if there are statements, false otherwise
     */
    public boolean hasStatements() {
        return initialSize > 0;
    }

    /**
     * Checks if there are any used statements in the Nanopub.
     *
     * @return true if there are used statements, false otherwise
     */
    public boolean hasUsedStatements() {
        return unusedStatements.size() < initialSize;
    }

    /**
     * Checks if there are any unused statements in the Nanopub.
     *
     * @return true if there are unused statements, false otherwise
     */
    public boolean hasUnusedStatements() {
        return !unusedStatements.isEmpty();
    }

    /**
     * Returns the list of unused statements in the Nanopub.
     *
     * @return the list of unused statements
     */
    public List<Statement> getUnusedStatements() {
        return unusedStatements;
    }

    /**
     * Removes a specific unused statement from the list.
     *
     * @param st the statement to remove
     */
    public void removeUnusedStatement(Statement st) {
        unusedStatements.remove(st);
    }

    /**
     * Removes unused statements based on the specified subject, predicate, and object.
     *
     * @param subj the subject to match, can be null
     * @param pred the predicate to match, can be null
     * @param obj  the object to match, can be null
     */
    public void removeUnusedStatements(IRI subj, IRI pred, Value obj) {
        for (Statement st : new ArrayList<>(unusedStatements)) {
            if (subj != null && !st.getSubject().equals(subj)) continue;
            if (pred != null && !st.getPredicate().equals(pred)) continue;
            if (obj != null && !st.getObject().equals(obj)) continue;
            unusedStatements.remove(st);
        }
    }

    Statement transform(Statement st) {
        if (formMode && st.getContext().equals(fillNp.getPubinfoUri())) {
            IRI pred = st.getPredicate();
            // TODO We might want to filter some of these out afterwards in PublishForm, to be more precise:
            if (st.getSubject().equals(fillNp.getUri())) {
                if (pred.equals(DCTERMS.CREATED)) return null;
                if (pred.equals(NPX.SUPERSEDES)) return null;
                if (pred.equals(RDFS.LABEL)) return null;
                if (pred.equals(NPX.INTRODUCES)) return null;
                if (pred.equals(NPX.EMBEDS)) return null;
                if (pred.equals(NPX.WAS_CREATED_AT)) return null;
                if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_TEMPLATE)) return null;
                if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_PROVENANCE_TEMPLATE)) return null;
                if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_PUBINFO_TEMPLATE)) return null;
            }
            if (pred.equals(NPX.HAS_ALGORITHM)) return null;
            if (pred.equals(NPX.HAS_PUBLIC_KEY)) return null;
            if (pred.equals(NPX.HAS_SIGNATURE)) return null;
            if (pred.equals(NPX.HAS_SIGNATURE_TARGET)) return null;
            if (pred.equals(NPX.SIGNED_BY)) return null;
            if (pred.equals(NTEMPLATE.HAS_LABEL_FROM_API)) {
                GuidedChoiceItem.setLabel(st.getSubject().stringValue(), st.getObject().stringValue());
                return null;
            }
            if (pred.equals(RDFS.LABEL)) {
                GuidedChoiceItem.setLabel(st.getSubject().stringValue(), st.getObject().stringValue());
            }
        }
        return vf.createStatement(
                (Resource) transform(st.getSubject()),
                (IRI) transform(st.getPredicate()),
                transform(st.getObject()),
                (Resource) transform(st.getContext()));
    }

    Value transform(Value v) {
        if (fillNp.getUri().equals(v)) {
            return LocalUri.of("nanopub");
        } else if (fillNp.getAssertionUri().equals(v)) {
            return LocalUri.of("assertion");
        } else if (v instanceof IRI iri && formMode) {
            if (!NanopubUtils.getIntroducedIriIds(fillNp).contains(iri.stringValue()) || fillMode != FillMode.SUPERSEDE) {
                if (v.stringValue().startsWith(fillNp.getUri().stringValue())) {
                    return LocalUri.of(Utils.getUriPostfix(v.stringValue()));
                }
            }
        }
        return v;
    }

}

1	package com.knowledgepixels.nanodash.template;
2
3	import com.knowledgepixels.nanodash.LocalUri;
4	import com.knowledgepixels.nanodash.Utils;
5	import com.knowledgepixels.nanodash.component.GuidedChoiceItem;
6	import com.knowledgepixels.nanodash.component.PublishForm.FillMode;
7	import org.eclipse.rdf4j.model.*;
8	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
9	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
10	import org.eclipse.rdf4j.model.vocabulary.RDFS;
11	import org.nanopub.Nanopub;
12	import org.nanopub.NanopubUtils;
13	import org.nanopub.vocabulary.NPX;
14	import org.nanopub.vocabulary.NTEMPLATE;
15	import org.slf4j.Logger;
16	import org.slf4j.LoggerFactory;
17
18	import java.util.ArrayList;
19	import java.util.List;
20	import java.util.Set;
21
22	/**
23	* ValueFiller is a utility class that processes a Nanopub and fills a TemplateContext.
24	*/
25	public class ValueFiller {
26
27	private static ValueFactory vf = SimpleValueFactory.getInstance();	6✔
28
29	private Nanopub fillNp;
30	private FillMode fillMode;
31	private List<Statement> unusedStatements = new ArrayList<>();	15✔
32	private int initialSize;
33	private boolean formMode;
34	private static final Logger logger = LoggerFactory.getLogger(ValueFiller.class);	12✔
35
36	/**
37	* Constructor for ValueFiller.
38	*
39	* @param fillNp the Nanopub to fill
40	* @param contextType the type of context to fill
41	* @param formMode if true, the filler will adapt to form mode, filtering out certain statements
42	*/
43	public ValueFiller(Nanopub fillNp, ContextType contextType, boolean formMode) {
44	this(fillNp, contextType, formMode, null);	18✔
45	}	3✔
46
47	/**
48	* Constructor for ValueFiller with specified fill mode.
49	*
50	* @param fillNp the Nanopub to fill
51	* @param contextType the type of context to fill
52	* @param formMode if true, the filler will adapt to form mode, filtering out certain statements
53	* @param fillMode the fill mode to use, can be null for default behavior
54	*/
55	public ValueFiller(Nanopub fillNp, ContextType contextType, boolean formMode, FillMode fillMode) {	6✔
56	this.fillNp = fillNp;	9✔
57	this.formMode = formMode;	9✔
58	this.fillMode = fillMode;	9✔
59	Set<Statement> statements;
60	if (contextType == ContextType.ASSERTION) {	9!
61	statements = fillNp.getAssertion();	12✔
62	} else if (contextType == ContextType.PROVENANCE) {	×
63	statements = fillNp.getProvenance();	×
64	} else {
65	statements = fillNp.getPubinfo();	×
66	}
67	for (Statement st : statements) {	30✔
68	Statement stT = transform(st);	12✔
69	if (stT != null) unusedStatements.add(stT);	21!
70	}	3✔
71	unusedStatements.sort((st1, st2) -> {	12✔
72	String st1s = st1.getSubject() + " " + st1.getPredicate() + " " + st1.getObject();	×
73	String st2s = st2.getSubject() + " " + st2.getPredicate() + " " + st2.getObject();	×
74	return st1s.compareTo(st2s);	×
75	});
76	initialSize = unusedStatements.size();	15✔
77	}	3✔
78
79	/**
80	* Fills the TemplateContext with the unused statements.
81	*
82	* @param context the TemplateContext to fill
83	*/
84	public void fill(TemplateContext context) {
85	try {
86	context.fill(unusedStatements);	×
87	} catch (UnificationException ex) {	×
88	logger.error("Could not fill template context", ex);	×
89	}	×
90	}	×
91
92	/**
93	* Checks if the Nanopub has any statements.
94	*
95	* @return true if there are statements, false otherwise
96	*/
97	public boolean hasStatements() {
98	return initialSize > 0;	18!
99	}
100
101	/**
102	* Checks if there are any used statements in the Nanopub.
103	*
104	* @return true if there are used statements, false otherwise
105	*/
106	public boolean hasUsedStatements() {
107	return unusedStatements.size() < initialSize;	24!
108	}
109
110	/**
111	* Checks if there are any unused statements in the Nanopub.
112	*
113	* @return true if there are unused statements, false otherwise
114	*/
115	public boolean hasUnusedStatements() {
116	return !unusedStatements.isEmpty();	21!
117	}
118
119	/**
120	* Returns the list of unused statements in the Nanopub.
121	*
122	* @return the list of unused statements
123	*/
124	public List<Statement> getUnusedStatements() {
125	return unusedStatements;	9✔
126	}
127
128	/**
129	* Removes a specific unused statement from the list.
130	*
131	* @param st the statement to remove
132	*/
133	public void removeUnusedStatement(Statement st) {
134	unusedStatements.remove(st);	×
135	}	×
136
137	/**
138	* Removes unused statements based on the specified subject, predicate, and object.
139	*
140	* @param subj the subject to match, can be null
141	* @param pred the predicate to match, can be null
142	* @param obj the object to match, can be null
143	*/
144	public void removeUnusedStatements(IRI subj, IRI pred, Value obj) {
145	for (Statement st : new ArrayList<>(unusedStatements)) {	×
146	if (subj != null && !st.getSubject().equals(subj)) continue;	×
147	if (pred != null && !st.getPredicate().equals(pred)) continue;	×
148	if (obj != null && !st.getObject().equals(obj)) continue;	×
149	unusedStatements.remove(st);	×
150	}	×
151	}	×
152
153	Statement transform(Statement st) {
154	if (formMode && st.getContext().equals(fillNp.getPubinfoUri())) {	30!
155	IRI pred = st.getPredicate();	×
156	// TODO We might want to filter some of these out afterwards in PublishForm, to be more precise:
157	if (st.getSubject().equals(fillNp.getUri())) {	×
158	if (pred.equals(DCTERMS.CREATED)) return null;	×
159	if (pred.equals(NPX.SUPERSEDES)) return null;	×
160	if (pred.equals(RDFS.LABEL)) return null;	×
161	if (pred.equals(NPX.INTRODUCES)) return null;	×
162	if (pred.equals(NPX.EMBEDS)) return null;	×
163	if (pred.equals(NPX.WAS_CREATED_AT)) return null;	×
164	if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_TEMPLATE)) return null;	×
165	if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_PROVENANCE_TEMPLATE)) return null;	×
166	if (pred.equals(NTEMPLATE.WAS_CREATED_FROM_PUBINFO_TEMPLATE)) return null;	×
167	}
168	if (pred.equals(NPX.HAS_ALGORITHM)) return null;	×
169	if (pred.equals(NPX.HAS_PUBLIC_KEY)) return null;	×
170	if (pred.equals(NPX.HAS_SIGNATURE)) return null;	×
171	if (pred.equals(NPX.HAS_SIGNATURE_TARGET)) return null;	×
172	if (pred.equals(NPX.SIGNED_BY)) return null;	×
173	if (pred.equals(NTEMPLATE.HAS_LABEL_FROM_API)) {	×
174	GuidedChoiceItem.setLabel(st.getSubject().stringValue(), st.getObject().stringValue());	×
175	return null;	×
176	}
177	if (pred.equals(RDFS.LABEL)) {	×
178	GuidedChoiceItem.setLabel(st.getSubject().stringValue(), st.getObject().stringValue());	×
179	}
180	}
181	return vf.createStatement(	15✔
182	(Resource) transform(st.getSubject()),	15✔
183	(IRI) transform(st.getPredicate()),	15✔
184	transform(st.getObject()),	12✔
185	(Resource) transform(st.getContext()));	9✔
186	}
187
188	Value transform(Value v) {
189	if (fillNp.getUri().equals(v)) {	18✔
190	return LocalUri.of("nanopub");	9✔
191	} else if (fillNp.getAssertionUri().equals(v)) {	18✔
192	return LocalUri.of("assertion");	9✔
193	} else if (v instanceof IRI iri && formMode) {	27!
194	if (!NanopubUtils.getIntroducedIriIds(fillNp).contains(iri.stringValue()) \|\| fillMode != FillMode.SUPERSEDE) {	21!
195	if (v.stringValue().startsWith(fillNp.getUri().stringValue())) {	24!
196	return LocalUri.of(Utils.getUriPostfix(v.stringValue()));	×
197	}
198	}
199	}
200	return v;	6✔
201	}
202
203	}

knowledgepixels / nanodash / 20268226543

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