18557556913

Committed 16 Oct 2025 10:00AM UTC coverage: 13.57% (-0.04%) from 13.607%

Build # 18557556913

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push

github

Committed by

tkuhn

Commit Message

fix: Properly treat introduced resources that are not URI placeholders

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

package com.knowledgepixels.nanodash.template;

import com.knowledgepixels.nanodash.NanodashSession;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.PublishForm.FillMode;
import com.knowledgepixels.nanodash.component.StatementItem;
import org.apache.wicket.Component;
import org.apache.wicket.model.IModel;
import org.apache.wicket.model.Model;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.nanopub.*;
import org.nanopub.vocabulary.NTEMPLATE;

import java.io.Serializable;
import java.util.*;

/**
 * Context for a template, containing all necessary information to fill.
 */
public class TemplateContext implements Serializable {

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    private final ContextType contextType;
    private final Template template;
    private final String componentId;
    private final Map<String, String> params = new HashMap<>();
    private List<Component> components = new ArrayList<>();
    private Map<IRI, IModel<String>> componentModels = new HashMap<>();
    private Set<IRI> introducedIris = new HashSet<>();
    private Set<IRI> embeddedIris = new HashSet<>();
    private List<StatementItem> statementItems;
    private Set<IRI> iriSet = new HashSet<>();
    private Map<IRI, StatementItem> narrowScopeMap = new HashMap<>();
    private String targetNamespace = Template.DEFAULT_TARGET_NAMESPACE;
    private Nanopub existingNanopub;
    private Map<IRI, String> labels;
    private FillMode fillMode = null;

    /**
     * Constructor for creating a new template context for filling a template.
     *
     * @param contextType     the type of context
     * @param templateId      the ID of the template to fill
     * @param componentId     the ID of the component that will use this context
     * @param targetNamespace the target namespace for the template, can be null to use the default namespace
     */
    public TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace) {
        this(contextType, templateId, componentId, targetNamespace, null);
    }

    /**
     * Constructor for creating a new template context for filling a template.
     *
     * @param contextType     the type of context
     * @param templateId      the ID of the template to fill
     * @param componentId     the ID of the component that will use this context
     * @param existingNanopub an existing nanopub to fill, can be null if creating a new nanopub
     */
    public TemplateContext(ContextType contextType, String templateId, String componentId, Nanopub existingNanopub) {
        this(contextType, templateId, componentId, null, existingNanopub);
    }

    private TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace, Nanopub existingNanopub) {
        this.contextType = contextType;
        // TODO: check whether template is of correct type:
        this.template = TemplateData.get().getTemplate(templateId);
        this.componentId = componentId;
        if (targetNamespace != null) {
            this.targetNamespace = targetNamespace;
        }
        this.existingNanopub = existingNanopub;
        if (existingNanopub == null && NanodashSession.get().getUserIri() != null) {
            componentModels.put(NTEMPLATE.CREATOR_PLACEHOLDER, Model.of(NanodashSession.get().getUserIri().stringValue()));
        }
    }

    /**
     * Initializes the statements for this context.
     */
    public void initStatements() {
        if (statementItems != null) return;
        statementItems = new ArrayList<>();
        for (IRI st : template.getStatementIris()) {
            StatementItem si = new StatementItem(componentId, st, this);
            statementItems.add(si);
            for (IRI i : si.getIriSet()) {
                if (iriSet.contains(i)) {
                    narrowScopeMap.remove(i);
                } else {
                    iriSet.add(i);
                    narrowScopeMap.put(i, si);
                }
            }
        }
    }

    /**
     * Finalizes the statements by processing all parameters and setting the repetition counts.
     */
    public void finalizeStatements() {
        Map<StatementItem, Integer> finalRepetitionCount = new HashMap<>();
        for (IRI ni : narrowScopeMap.keySet()) {
            // TODO: Move all occurrences of this to utility function:
            String postfix = Utils.getUriPostfix(ni);
            StatementItem si = narrowScopeMap.get(ni);
            int i = si.getRepetitionCount();
            while (true) {
                String p = postfix + "__" + i;
                if (hasParam(p)) {
                    si.addRepetitionGroup();
                } else {
                    break;
                }
                i++;
            }
            i = 1;
            int corr = 0;
            if (si.isEmpty()) corr = 1;
            while (true) {
                String p = postfix + "__." + i;
                if (hasParam(p)) {
                    int absPos = si.getRepetitionCount() + i - 1 - corr;
                    String param = postfix + "__" + absPos;
                    if (i - corr == 0) param = postfix;
                    setParam(param, getParam(p));
                    finalRepetitionCount.put(si, i - corr);
                } else {
                    break;
                }
                i++;
            }
        }
        for (StatementItem si : finalRepetitionCount.keySet()) {
            for (int i = 0; i < finalRepetitionCount.get(si); i++) {
                si.addRepetitionGroup();
            }
        }
        for (StatementItem si : statementItems) {
            si.finalizeValues();
        }
    }

    /**
     * Sets the fill mode for this context.
     *
     * @param fillMode the fill mode to set
     */
    public void setFillMode(FillMode fillMode) {
        this.fillMode = fillMode;
    }

    /**
     * Gets the fill mode for this context.
     *
     * @return the fill mode, or null if not set
     */
    public FillMode getFillMode() {
        return fillMode;
    }

    /**
     * Returns the type of context.
     *
     * @return the context type
     */
    public ContextType getType() {
        return contextType;
    }

    /**
     * Returns the template associated with this context.
     *
     * @return the template
     */
    public Template getTemplate() {
        return template;
    }

    /**
     * Returns the ID of the template associated with this context.
     *
     * @return the template ID
     */
    public String getTemplateId() {
        return template.getId();
    }

    /**
     * Sets a parameter for this context.
     *
     * @param name  the name of the parameter
     * @param value the value of the parameter
     */
    public void setParam(String name, String value) {
        params.put(name, value);
    }

    /**
     * Gets a parameter value by its name.
     *
     * @param name the name of the parameter
     * @return the value of the parameter, or null if not set
     */
    public String getParam(String name) {
        return params.get(name);
    }

    /**
     * Checks if a parameter with the given name exists.
     *
     * @param name the name of the parameter
     * @return true if the parameter exists, false otherwise
     */
    public boolean hasParam(String name) {
        return params.containsKey(name);
    }

    /**
     * Returns the components associated with this context.
     *
     * @return a list of components
     */
    public List<Component> getComponents() {
        return components;
    }

    /**
     * Returns the component models associated with this context.
     *
     * @return a map of IRI to model of strings
     */
    public Map<IRI, IModel<String>> getComponentModels() {
        return componentModels;
    }

    /**
     * Returns the introduced IRIs in this context.
     *
     * @return a set of introduced IRIs
     */
    public Set<IRI> getIntroducedIris() {
        return introducedIris;
    }

    /**
     * Returns the embedded IRIs in this context.
     *
     * @return a set of embedded IRIs
     */
    public Set<IRI> getEmbeddedIris() {
        return embeddedIris;
    }

    /**
     * Processes an IRI by applying the template's processing rules.
     *
     * @param iri the IRI to process
     * @return the processed IRI, or null if the processing results in no value
     */
    public IRI processIri(IRI iri) {
        Value v = processValue(iri);
        if (v == null) return null;
        if (v instanceof IRI) return (IRI) v;
        return iri;
    }

    /**
     * Processes a Value according to the template's rules.
     *
     * @param value the Value to process
     * @return the processed Value, or the original Value if no processing is applicable
     */
    public Value processValue(Value value) {
        if (!(value instanceof IRI)) return value;
        IRI iri = (IRI) value;
        if (iri.equals(NTEMPLATE.CREATOR_PLACEHOLDER)) {
            iri = NanodashSession.get().getUserIri();
        }
        if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {
            iri = vf.createIRI(targetNamespace + "assertion");
        } else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {
            iri = vf.createIRI(targetNamespace);
        }
        // TODO: Move this code below to the respective placeholder classes:
        IModel<String> tf = componentModels.get(iri);
        Value processedValue = null;
        if (template.isRestrictedChoicePlaceholder(iri)) {
            if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                String prefix = template.getPrefix(iri);
                if (prefix == null) prefix = "";
                if (template.isLocalResource(iri)) prefix = targetNamespace;
                if (tf.getObject().matches("https?://.+")) prefix = "";
                String v = prefix + tf.getObject();
                if (v.matches("[^:# ]+")) v = targetNamespace + v;
                if (v.matches("https?://.*")) {
                    processedValue = vf.createIRI(v);
                } else {
                    processedValue = vf.createLiteral(tf.getObject());
                }
            }
        } else if (template.isUriPlaceholder(iri)) {
            if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                String prefix = template.getPrefix(iri);
                if (prefix == null) prefix = "";
                if (template.isLocalResource(iri)) prefix = targetNamespace;
                String v;
                if (template.isAutoEscapePlaceholder(iri)) {
                    v = prefix + Utils.urlEncode(tf.getObject());
                } else {
                    if (tf.getObject().matches("https?://.+")) prefix = "";
                    v = prefix + tf.getObject();
                }
                if (v.matches("[^:# ]+")) v = targetNamespace + v;
                processedValue = vf.createIRI(v);
            }
        } else if (template.isLocalResource(iri)) {
            if (template.isIntroducedResource(iri) && fillMode == FillMode.SUPERSEDE) {
                if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                    processedValue = vf.createIRI(tf.getObject());
                }
            } else {
                String prefix = Utils.getUriPrefix(iri);
                processedValue = vf.createIRI(iri.stringValue().replace(prefix, targetNamespace));
            }
        } else if (template.isLiteralPlaceholder(iri)) {
            IRI datatype = template.getDatatype(iri);
            String languagetag = template.getLanguageTag(iri);
            if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                if (datatype != null) {
                    processedValue = vf.createLiteral(tf.getObject(), datatype);
                } else if (languagetag != null) {
                    processedValue = vf.createLiteral(tf.getObject(), languagetag);
                } else {
                    processedValue = vf.createLiteral(tf.getObject());
                }
            }

        } else if (template.isValuePlaceholder(iri)) {
            if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                if (Utils.isValidLiteralSerialization(tf.getObject())) {
                    processedValue = Utils.getParsedLiteral(tf.getObject());
                } else {
                    String v = tf.getObject();
                    if (v.matches("[^:# ]+")) v = targetNamespace + v;
                    processedValue = vf.createIRI(v);
                }
            }
        } else if (template.isSequenceElementPlaceholder(iri)) {
            if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {
                processedValue = vf.createIRI(tf.getObject());
            }
        } else {
            processedValue = iri;
        }
        if (processedValue instanceof IRI pvIri && template.isIntroducedResource(iri)) {
            introducedIris.add(pvIri);
        }
        if (processedValue instanceof IRI pvIri && template.isEmbeddedResource(iri)) {
            embeddedIris.add(pvIri);
        }
        return processedValue;
    }

    /**
     * Returns the statement items associated with this context.
     *
     * @return a list of StatementItem objects
     */
    public List<StatementItem> getStatementItems() {
        return statementItems;
    }

    /**
     * Propagates the statements from this context to a NanopubCreator.
     *
     * @param npCreator the NanopubCreator to which the statements will be added
     * @throws org.nanopub.MalformedNanopubException        if there is an error in the nanopub structure
     * @throws org.nanopub.NanopubAlreadyFinalizedException if the nanopub has already been finalized
     */
    public void propagateStatements(NanopubCreator npCreator) throws MalformedNanopubException, NanopubAlreadyFinalizedException {
        if (template.getNanopub() instanceof NanopubWithNs) {
            NanopubWithNs np = (NanopubWithNs) template.getNanopub();
            for (String p : np.getNsPrefixes()) {
                npCreator.addNamespace(p, np.getNamespace(p));
            }
        }
        for (StatementItem si : statementItems) {
            si.addTriplesTo(npCreator);
        }
    }

    /**
     * Checks if the context has a narrow scope for the given IRI.
     *
     * @param iri the IRI to check
     * @return true if there is a narrow scope for the IRI, false otherwise
     */
    public boolean hasNarrowScope(IRI iri) {
        return narrowScopeMap.containsKey(iri);
    }

    /**
     * Checks if any of the statement items in this context will match any triple.
     *
     * @return true if any statement item will match any triple, false otherwise
     */
    public boolean willMatchAnyTriple() {
        initStatements();
        for (StatementItem si : statementItems) {
            if (si.willMatchAnyTriple()) return true;
        }
        return false;
    }

    /**
     * Fills the context with statements, processing each StatementItem.
     *
     * @param statements the list of statements to fill
     * @throws com.knowledgepixels.nanodash.template.UnificationException if there is an error during unification of statements
     */
    public void fill(List<Statement> statements) throws UnificationException {
        for (StatementItem si : statementItems) {
            si.fill(statements);
        }
        for (StatementItem si : statementItems) {
            si.fillFinished();
        }
    }

    /**
     * Returns the existing Nanopub associated with this context, if any.
     *
     * @return the existing Nanopub, or null if this context is for a new Nanopub
     */
    public Nanopub getExistingNanopub() {
        return existingNanopub;
    }

    /**
     * Checks if this context is read-only.
     *
     * @return true if the context is read-only, false otherwise
     */
    public boolean isReadOnly() {
        return existingNanopub != null;
    }

    /**
     * Returns the label for a given IRI, if available.
     *
     * @param iri the IRI for which to get the label
     * @return the label as a String, or null if no label is found
     */
    public String getLabel(IRI iri) {
        if (existingNanopub == null) return null;
        if (labels == null) {
            labels = new HashMap<>();
            for (Statement st : existingNanopub.getPubinfo()) {
                if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) || st.getPredicate().equals(RDFS.LABEL)) {
                    String label = st.getObject().stringValue();
                    labels.put((IRI) st.getSubject(), label);
                }
            }
        }
        return labels.get(iri);
    }

}

1	package com.knowledgepixels.nanodash.template;
2
3	import com.knowledgepixels.nanodash.NanodashSession;
4	import com.knowledgepixels.nanodash.Utils;
5	import com.knowledgepixels.nanodash.component.PublishForm.FillMode;
6	import com.knowledgepixels.nanodash.component.StatementItem;
7	import org.apache.wicket.Component;
8	import org.apache.wicket.model.IModel;
9	import org.apache.wicket.model.Model;
10	import org.eclipse.rdf4j.model.IRI;
11	import org.eclipse.rdf4j.model.Statement;
12	import org.eclipse.rdf4j.model.Value;
13	import org.eclipse.rdf4j.model.ValueFactory;
14	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
15	import org.eclipse.rdf4j.model.vocabulary.RDFS;
16	import org.nanopub.*;
17	import org.nanopub.vocabulary.NTEMPLATE;
18
19	import java.io.Serializable;
20	import java.util.*;
21
22	/**
23	* Context for a template, containing all necessary information to fill.
24	*/
25	public class TemplateContext implements Serializable {
26
27	private static ValueFactory vf = SimpleValueFactory.getInstance();	3✔
28
29	private final ContextType contextType;
30	private final Template template;
31	private final String componentId;
32	private final Map<String, String> params = new HashMap<>();	×
33	private List<Component> components = new ArrayList<>();	×
34	private Map<IRI, IModel<String>> componentModels = new HashMap<>();	×
35	private Set<IRI> introducedIris = new HashSet<>();	×
36	private Set<IRI> embeddedIris = new HashSet<>();	×
37	private List<StatementItem> statementItems;
38	private Set<IRI> iriSet = new HashSet<>();	×
39	private Map<IRI, StatementItem> narrowScopeMap = new HashMap<>();	×
40	private String targetNamespace = Template.DEFAULT_TARGET_NAMESPACE;	×
41	private Nanopub existingNanopub;
42	private Map<IRI, String> labels;
43	private FillMode fillMode = null;	×
44
45	/**
46	* Constructor for creating a new template context for filling a template.
47	*
48	* @param contextType the type of context
49	* @param templateId the ID of the template to fill
50	* @param componentId the ID of the component that will use this context
51	* @param targetNamespace the target namespace for the template, can be null to use the default namespace
52	*/
53	public TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace) {
54	this(contextType, templateId, componentId, targetNamespace, null);	×
55	}	×
56
57	/**
58	* Constructor for creating a new template context for filling a template.
59	*
60	* @param contextType the type of context
61	* @param templateId the ID of the template to fill
62	* @param componentId the ID of the component that will use this context
63	* @param existingNanopub an existing nanopub to fill, can be null if creating a new nanopub
64	*/
65	public TemplateContext(ContextType contextType, String templateId, String componentId, Nanopub existingNanopub) {
66	this(contextType, templateId, componentId, null, existingNanopub);	×
67	}	×
68
69	private TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace, Nanopub existingNanopub) {	×
70	this.contextType = contextType;	×
71	// TODO: check whether template is of correct type:
72	this.template = TemplateData.get().getTemplate(templateId);	×
73	this.componentId = componentId;	×
74	if (targetNamespace != null) {	×
75	this.targetNamespace = targetNamespace;	×
76	}
77	this.existingNanopub = existingNanopub;	×
78	if (existingNanopub == null && NanodashSession.get().getUserIri() != null) {	×
79	componentModels.put(NTEMPLATE.CREATOR_PLACEHOLDER, Model.of(NanodashSession.get().getUserIri().stringValue()));	×
80	}
81	}	×
82
83	/**
84	* Initializes the statements for this context.
85	*/
86	public void initStatements() {
87	if (statementItems != null) return;	×
88	statementItems = new ArrayList<>();	×
89	for (IRI st : template.getStatementIris()) {	×
90	StatementItem si = new StatementItem(componentId, st, this);	×
91	statementItems.add(si);	×
92	for (IRI i : si.getIriSet()) {	×
93	if (iriSet.contains(i)) {	×
94	narrowScopeMap.remove(i);	×
95	} else {
96	iriSet.add(i);	×
97	narrowScopeMap.put(i, si);	×
98	}
99	}	×
100	}	×
101	}	×
102
103	/**
104	* Finalizes the statements by processing all parameters and setting the repetition counts.
105	*/
106	public void finalizeStatements() {
107	Map<StatementItem, Integer> finalRepetitionCount = new HashMap<>();	×
108	for (IRI ni : narrowScopeMap.keySet()) {	×
109	// TODO: Move all occurrences of this to utility function:
110	String postfix = Utils.getUriPostfix(ni);	×
111	StatementItem si = narrowScopeMap.get(ni);	×
112	int i = si.getRepetitionCount();	×
113	while (true) {
114	String p = postfix + "__" + i;	×
115	if (hasParam(p)) {	×
116	si.addRepetitionGroup();	×
117	} else {
118	break;
119	}
120	i++;	×
121	}	×
122	i = 1;	×
123	int corr = 0;	×
124	if (si.isEmpty()) corr = 1;	×
125	while (true) {
126	String p = postfix + "__." + i;	×
127	if (hasParam(p)) {	×
128	int absPos = si.getRepetitionCount() + i - 1 - corr;	×
129	String param = postfix + "__" + absPos;	×
130	if (i - corr == 0) param = postfix;	×
131	setParam(param, getParam(p));	×
132	finalRepetitionCount.put(si, i - corr);	×
133	} else {
134	break;
135	}
136	i++;	×
137	}	×
138	}	×
139	for (StatementItem si : finalRepetitionCount.keySet()) {	×
140	for (int i = 0; i < finalRepetitionCount.get(si); i++) {	×
141	si.addRepetitionGroup();	×
142	}
143	}	×
144	for (StatementItem si : statementItems) {	×
145	si.finalizeValues();	×
146	}	×
147	}	×
148
149	/**
150	* Sets the fill mode for this context.
151	*
152	* @param fillMode the fill mode to set
153	*/
154	public void setFillMode(FillMode fillMode) {
155	this.fillMode = fillMode;	×
156	}	×
157
158	/**
159	* Gets the fill mode for this context.
160	*
161	* @return the fill mode, or null if not set
162	*/
163	public FillMode getFillMode() {
164	return fillMode;	×
165	}
166
167	/**
168	* Returns the type of context.
169	*
170	* @return the context type
171	*/
172	public ContextType getType() {
173	return contextType;	×
174	}
175
176	/**
177	* Returns the template associated with this context.
178	*
179	* @return the template
180	*/
181	public Template getTemplate() {
182	return template;	×
183	}
184
185	/**
186	* Returns the ID of the template associated with this context.
187	*
188	* @return the template ID
189	*/
190	public String getTemplateId() {
191	return template.getId();	×
192	}
193
194	/**
195	* Sets a parameter for this context.
196	*
197	* @param name the name of the parameter
198	* @param value the value of the parameter
199	*/
200	public void setParam(String name, String value) {
201	params.put(name, value);	×
202	}	×
203
204	/**
205	* Gets a parameter value by its name.
206	*
207	* @param name the name of the parameter
208	* @return the value of the parameter, or null if not set
209	*/
210	public String getParam(String name) {
211	return params.get(name);	×
212	}
213
214	/**
215	* Checks if a parameter with the given name exists.
216	*
217	* @param name the name of the parameter
218	* @return true if the parameter exists, false otherwise
219	*/
220	public boolean hasParam(String name) {
221	return params.containsKey(name);	×
222	}
223
224	/**
225	* Returns the components associated with this context.
226	*
227	* @return a list of components
228	*/
229	public List<Component> getComponents() {
230	return components;	×
231	}
232
233	/**
234	* Returns the component models associated with this context.
235	*
236	* @return a map of IRI to model of strings
237	*/
238	public Map<IRI, IModel<String>> getComponentModels() {
239	return componentModels;	×
240	}
241
242	/**
243	* Returns the introduced IRIs in this context.
244	*
245	* @return a set of introduced IRIs
246	*/
247	public Set<IRI> getIntroducedIris() {
248	return introducedIris;	×
249	}
250
251	/**
252	* Returns the embedded IRIs in this context.
253	*
254	* @return a set of embedded IRIs
255	*/
256	public Set<IRI> getEmbeddedIris() {
257	return embeddedIris;	×
258	}
259
260	/**
261	* Processes an IRI by applying the template's processing rules.
262	*
263	* @param iri the IRI to process
264	* @return the processed IRI, or null if the processing results in no value
265	*/
266	public IRI processIri(IRI iri) {
267	Value v = processValue(iri);	×
268	if (v == null) return null;	×
269	if (v instanceof IRI) return (IRI) v;	×
270	return iri;	×
271	}
272
273	/**
274	* Processes a Value according to the template's rules.
275	*
276	* @param value the Value to process
277	* @return the processed Value, or the original Value if no processing is applicable
278	*/
279	public Value processValue(Value value) {
280	if (!(value instanceof IRI)) return value;	×
281	IRI iri = (IRI) value;	×
282	if (iri.equals(NTEMPLATE.CREATOR_PLACEHOLDER)) {	×
283	iri = NanodashSession.get().getUserIri();	×
284	}
285	if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {	×
286	iri = vf.createIRI(targetNamespace + "assertion");	×
287	} else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {	×
288	iri = vf.createIRI(targetNamespace);	×
289	}
290	// TODO: Move this code below to the respective placeholder classes:
291	IModel<String> tf = componentModels.get(iri);	×
292	Value processedValue = null;	×
293	if (template.isRestrictedChoicePlaceholder(iri)) {	×
294	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
295	String prefix = template.getPrefix(iri);	×
296	if (prefix == null) prefix = "";	×
297	if (template.isLocalResource(iri)) prefix = targetNamespace;	×
298	if (tf.getObject().matches("https?://.+")) prefix = "";	×
299	String v = prefix + tf.getObject();	×
300	if (v.matches("[^:# ]+")) v = targetNamespace + v;	×
301	if (v.matches("https?://.*")) {	×
302	processedValue = vf.createIRI(v);	×
303	} else {
304	processedValue = vf.createLiteral(tf.getObject());	×
305	}
306	}	×
307	} else if (template.isUriPlaceholder(iri)) {	×
308	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
309	String prefix = template.getPrefix(iri);	×
310	if (prefix == null) prefix = "";	×
311	if (template.isLocalResource(iri)) prefix = targetNamespace;	×
312	String v;
313	if (template.isAutoEscapePlaceholder(iri)) {	×
314	v = prefix + Utils.urlEncode(tf.getObject());	×
315	} else {
316	if (tf.getObject().matches("https?://.+")) prefix = "";	×
317	v = prefix + tf.getObject();	×
318	}
319	if (v.matches("[^:# ]+")) v = targetNamespace + v;	×
320	processedValue = vf.createIRI(v);	×
321	}	×
322	} else if (template.isLocalResource(iri)) {	×
323	if (template.isIntroducedResource(iri) && fillMode == FillMode.SUPERSEDE) {	×
324	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
325	processedValue = vf.createIRI(tf.getObject());	×
326	}
327	} else {
328	String prefix = Utils.getUriPrefix(iri);	×
329	processedValue = vf.createIRI(iri.stringValue().replace(prefix, targetNamespace));	×
330	}	×
331	} else if (template.isLiteralPlaceholder(iri)) {	×
332	IRI datatype = template.getDatatype(iri);	×
333	String languagetag = template.getLanguageTag(iri);	×
334	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
335	if (datatype != null) {	×
336	processedValue = vf.createLiteral(tf.getObject(), datatype);	×
337	} else if (languagetag != null) {	×
338	processedValue = vf.createLiteral(tf.getObject(), languagetag);	×
339	} else {
340	processedValue = vf.createLiteral(tf.getObject());	×
341	}
342	}
343
344	} else if (template.isValuePlaceholder(iri)) {	×
345	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
346	if (Utils.isValidLiteralSerialization(tf.getObject())) {	×
347	processedValue = Utils.getParsedLiteral(tf.getObject());	×
348	} else {
349	String v = tf.getObject();	×
350	if (v.matches("[^:# ]+")) v = targetNamespace + v;	×
351	processedValue = vf.createIRI(v);	×
352	}	×
353	}
354	} else if (template.isSequenceElementPlaceholder(iri)) {	×
355	if (tf != null && tf.getObject() != null && !tf.getObject().isEmpty()) {	×
356	processedValue = vf.createIRI(tf.getObject());	×
357	}
358	} else {
359	processedValue = iri;	×
360	}
361	if (processedValue instanceof IRI pvIri && template.isIntroducedResource(iri)) {	×
362	introducedIris.add(pvIri);	×
363	}
364	if (processedValue instanceof IRI pvIri && template.isEmbeddedResource(iri)) {	×
365	embeddedIris.add(pvIri);	×
366	}
367	return processedValue;	×
368	}
369
370	/**
371	* Returns the statement items associated with this context.
372	*
373	* @return a list of StatementItem objects
374	*/
375	public List<StatementItem> getStatementItems() {
376	return statementItems;	×
377	}
378
379	/**
380	* Propagates the statements from this context to a NanopubCreator.
381	*
382	* @param npCreator the NanopubCreator to which the statements will be added
383	* @throws org.nanopub.MalformedNanopubException if there is an error in the nanopub structure
384	* @throws org.nanopub.NanopubAlreadyFinalizedException if the nanopub has already been finalized
385	*/
386	public void propagateStatements(NanopubCreator npCreator) throws MalformedNanopubException, NanopubAlreadyFinalizedException {
387	if (template.getNanopub() instanceof NanopubWithNs) {	×
388	NanopubWithNs np = (NanopubWithNs) template.getNanopub();	×
389	for (String p : np.getNsPrefixes()) {	×
390	npCreator.addNamespace(p, np.getNamespace(p));	×
391	}	×
392	}
393	for (StatementItem si : statementItems) {	×
394	si.addTriplesTo(npCreator);	×
395	}	×
396	}	×
397
398	/**
399	* Checks if the context has a narrow scope for the given IRI.
400	*
401	* @param iri the IRI to check
402	* @return true if there is a narrow scope for the IRI, false otherwise
403	*/
404	public boolean hasNarrowScope(IRI iri) {
405	return narrowScopeMap.containsKey(iri);	×
406	}
407
408	/**
409	* Checks if any of the statement items in this context will match any triple.
410	*
411	* @return true if any statement item will match any triple, false otherwise
412	*/
413	public boolean willMatchAnyTriple() {
414	initStatements();	×
415	for (StatementItem si : statementItems) {	×
416	if (si.willMatchAnyTriple()) return true;	×
417	}	×
418	return false;	×
419	}
420
421	/**
422	* Fills the context with statements, processing each StatementItem.
423	*
424	* @param statements the list of statements to fill
425	* @throws com.knowledgepixels.nanodash.template.UnificationException if there is an error during unification of statements
426	*/
427	public void fill(List<Statement> statements) throws UnificationException {
428	for (StatementItem si : statementItems) {	×
429	si.fill(statements);	×
430	}	×
431	for (StatementItem si : statementItems) {	×
432	si.fillFinished();	×
433	}	×
434	}	×
435
436	/**
437	* Returns the existing Nanopub associated with this context, if any.
438	*
439	* @return the existing Nanopub, or null if this context is for a new Nanopub
440	*/
441	public Nanopub getExistingNanopub() {
442	return existingNanopub;	×
443	}
444
445	/**
446	* Checks if this context is read-only.
447	*
448	* @return true if the context is read-only, false otherwise
449	*/
450	public boolean isReadOnly() {
451	return existingNanopub != null;	×
452	}
453
454	/**
455	* Returns the label for a given IRI, if available.
456	*
457	* @param iri the IRI for which to get the label
458	* @return the label as a String, or null if no label is found
459	*/
460	public String getLabel(IRI iri) {
461	if (existingNanopub == null) return null;	×
462	if (labels == null) {	×
463	labels = new HashMap<>();	×
464	for (Statement st : existingNanopub.getPubinfo()) {	×
465	if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) \|\| st.getPredicate().equals(RDFS.LABEL)) {	×
466	String label = st.getObject().stringValue();	×
467	labels.put((IRI) st.getSubject(), label);	×
468	}
469	}	×
470	}
471	return labels.get(iri);	×
472	}
473
474	}

knowledgepixels / nanodash / 18557556913

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