17380144000

Committed 01 Sep 2025 02:12PM UTC coverage: 12.03% (+0.05%) from 11.978%

Build # 17380144000

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: replace printStackTrace with logger.error for better error handling

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33.54

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

package com.knowledgepixels.nanodash.template;

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 vf.createIRI("local:nanopub");
//                        return Template.NANOPUB_PLACEHOLDER;
        } else if (fillNp.getAssertionUri().equals(v)) {
            return vf.createIRI("local:assertion");
//                        return Template.ASSERTION_PLACEHOLDER;
        } 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 vf.createIRI("local:" + Utils.getUriPostfix(v.stringValue()));
                }
            }
        }
        return v;
    }

}

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

knowledgepixels / nanodash / 17380144000

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