19032518047

Committed 03 Nov 2025 11:10AM UTC coverage: 14.338% (-0.9%) from 15.251%

Build # 19032518047

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #269 from knowledgepixels/245-local-uri-without-slashes-or-hashes

Add check for local URIs to ensure that they don't contain slashes or hashes

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518 of 4518 branches covered (11.47%)

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1333 of 8392 relevant lines covered (15.88%)

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

knowledgepixels / nanodash / 19032518047

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