28111182502

Committed 24 Jun 2026 03:49PM UTC coverage: 26.584% (+0.03%) from 26.558%

Build # 28111182502

Build Type

Pull #504

github

Committed by

web-flow

Commit Message

Merge 5925d3a10 into 2a3e19dbb

Pull Request Pull Request #504: fix: don't abort the whole template fill on one unification failure

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

package com.knowledgepixels.nanodash.template;

import com.knowledgepixels.nanodash.LocalUri;
import com.knowledgepixels.nanodash.NanodashSession;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.LiteralDateItem;
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.eclipse.rdf4j.model.vocabulary.XSD;
import org.nanopub.*;
import org.nanopub.vocabulary.NTEMPLATE;

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

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

    private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(TemplateContext.class);
    private static final 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 final Map<IRI, IModel<?>> 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 Nanopub fillSource;
    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<?>> 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);
        } else if (template.isRootNanopubPlaceholder(iri)) {
            IModel<?> rootModel = componentModels.get(iri);
            String rootValue = (rootModel == null || rootModel.getObject() == null) ? "" : rootModel.getObject().toString();
            if (rootValue.equals(LocalUri.of("nanopub").stringValue())) {
                // Sentinel: in supersede/derive mode this means the existing nanopub was the root
                Nanopub ref = getReferenceNanopub();
                if (ref != null && (fillMode == FillMode.SUPERSEDE || fillMode == FillMode.DERIVE)) {
                    iri = vf.createIRI(ref.getUri().stringValue());
                } else {
                    iri = vf.createIRI(targetNamespace);
                }
            } else if (rootValue.isEmpty()) {
                iri = vf.createIRI(targetNamespace);
            } else {
                iri = vf.createIRI(rootValue);
            }
        }
        // TODO: Move this code below to the respective placeholder classes:
        IModel<?> tf = componentModels.get(iri);
        Value processedValue = null;
        Object tfObjectGeneric = null;
        if (tf != null) {
            tfObjectGeneric = tf.getObject();
        }
        if (template.isRestrictedChoicePlaceholder(iri)) {
            String tfObject = (String) tfObjectGeneric;
            if (tf != null && tfObject != null && !tfObject.isEmpty()) {
                String prefix = template.getPrefix(iri);
                if (prefix == null) prefix = "";
                if (template.isLocalResource(iri)) prefix = targetNamespace;
                if (tfObject.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(tfObject);
                }
            }
        } else if (template.isUriPlaceholder(iri)) {
            String tfObject = (String) tfObjectGeneric;
            if (tf != null && tfObject != null && !tfObject.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 (tfObject.matches("https?://.+")) prefix = "";
                    v = prefix + tf.getObject();
                }
                if (v.matches("[^:# ]+")) v = targetNamespace + v;
                processedValue = vf.createIRI(v);
            }
        } else if (template.isLocalResource(iri)) {
            String tfObject = (String) tfObjectGeneric;
            if (template.isIntroducedResource(iri) && fillMode == FillMode.SUPERSEDE) {
                if (tf != null && tfObject != null && !tfObject.isEmpty()) {
                    processedValue = vf.createIRI(tfObject);
                }
            } 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 (datatype != null) {
                if (datatype.equals(XSD.DATETIME)) {
                    ZonedDateTime tfObject = (ZonedDateTime) tfObjectGeneric;
                    if (tfObject != null) {
                        processedValue = vf.createLiteral(tfObject);
                    }
                } else if (datatype.equals(XSD.DATE)) {
                    Date tfObject = (Date) tfObjectGeneric;
                    if (tfObject != null) {
                        processedValue = vf.createLiteral(LiteralDateItem.format.format(tfObject), datatype);
                    }
                }
            } else {
                String tfObject = (String) tfObjectGeneric;
                if (tf != null && tfObject != null && !tfObject.isEmpty()) {
                    if (datatype != null) {
                        processedValue = vf.createLiteral(tfObject, datatype);
                    } else if (languageTag != null) {
                        processedValue = vf.createLiteral(tfObject, languageTag);
                    } else {
                        processedValue = vf.createLiteral(tfObject);
                    }
                }
            }
        } else if (template.isValuePlaceholder(iri)) {
            String tfObject = (String) tfObjectGeneric;
            if (tf != null && tfObject != null && !tfObject.isEmpty()) {
                if (Utils.isValidLiteralSerialization(tfObject)) {
                    processedValue = Utils.getParsedLiteral(tfObject);
                } else {
                    String v = tfObject;
                    if (v.matches("[^:# ]+")) v = targetNamespace + v;
                    processedValue = vf.createIRI(v);
                }
            }
        } else if (template.isSequenceElementPlaceholder(iri)) {
            String tfObject = (String) tfObjectGeneric;
            if (tf != null && tfObject != null && !tfObject.isEmpty()) {
                processedValue = vf.createIRI(tfObject);
            }
        } 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 UnificationException if there is an error during unification of statements
     */
    public void fill(List<Statement> statements) throws UnificationException {
        for (StatementItem si : statementItems) {
            // Isolate each statement: a unification failure on one must not abort the rest,
            // otherwise every later template statement is left unmatched. Roll back any partial
            // statement consumption so the next statement sees an intact pool.
            List<Statement> statementsBefore = new ArrayList<>(statements);
            try {
                si.fill(statements);
            } catch (UnificationException ex) {
                logger.warn("Could not fill statement; continuing with the remaining statements", ex);
                statements.clear();
                statements.addAll(statementsBefore);
            }
        }
        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;
    }

    /**
     * Returns the nanopub being used to fill this context (e.g. in supersede/derive
     * mode), if any. Unlike {@link #getExistingNanopub()} this does not imply the
     * context is read-only.
     *
     * @return the fill source nanopub, or null if none
     */
    public Nanopub getFillSource() {
        return fillSource;
    }

    /**
     * Sets the nanopub used to fill this context (e.g. in supersede/derive mode).
     *
     * @param fillSource the nanopub providing the values, or null to clear
     */
    public void setFillSource(Nanopub fillSource) {
        this.fillSource = fillSource;
    }

    /**
     * Returns the existing or fill-source nanopub for this context, preferring the
     * existing nanopub if set.
     *
     * @return the reference nanopub, or null if none
     */
    public Nanopub getReferenceNanopub() {
        return existingNanopub != null ? existingNanopub : fillSource;
    }

    /**
     * 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.LocalUri;
4	import com.knowledgepixels.nanodash.NanodashSession;
5	import com.knowledgepixels.nanodash.Utils;
6	import com.knowledgepixels.nanodash.component.LiteralDateItem;
7	import com.knowledgepixels.nanodash.component.PublishForm.FillMode;
8	import com.knowledgepixels.nanodash.component.StatementItem;
9	import org.apache.wicket.Component;
10	import org.apache.wicket.model.IModel;
11	import org.apache.wicket.model.Model;
12	import org.eclipse.rdf4j.model.IRI;
13	import org.eclipse.rdf4j.model.Statement;
14	import org.eclipse.rdf4j.model.Value;
15	import org.eclipse.rdf4j.model.ValueFactory;
16	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
17	import org.eclipse.rdf4j.model.vocabulary.RDFS;
18	import org.eclipse.rdf4j.model.vocabulary.XSD;
19	import org.nanopub.*;
20	import org.nanopub.vocabulary.NTEMPLATE;
21
22	import java.io.Serializable;
23	import java.time.ZonedDateTime;
24	import java.util.*;
25
26	/**
27	* Context for a template, containing all necessary information to fill.
28	*/
29	public class TemplateContext implements Serializable {
30
31	private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(TemplateContext.class);	9✔
32	private static final ValueFactory vf = SimpleValueFactory.getInstance();	9✔
33
34	private final ContextType contextType;
35	private final Template template;
36	private final String componentId;
37	private final Map<String, String> params = new HashMap<>();	15✔
38	private List<Component> components = new ArrayList<>();	15✔
39	private final Map<IRI, IModel<?>> componentModels = new HashMap<>();	15✔
40	private Set<IRI> introducedIris = new HashSet<>();	15✔
41	private Set<IRI> embeddedIris = new HashSet<>();	15✔
42	private List<StatementItem> statementItems;
43	private Set<IRI> iriSet = new HashSet<>();	15✔
44	private Map<IRI, StatementItem> narrowScopeMap = new HashMap<>();	15✔
45	private String targetNamespace = Template.DEFAULT_TARGET_NAMESPACE;	9✔
46	private Nanopub existingNanopub;
47	private Nanopub fillSource;
48	private Map<IRI, String> labels;
49	private FillMode fillMode = null;	9✔
50
51	/**
52	* Constructor for creating a new template context for filling a template.
53	*
54	* @param contextType the type of context
55	* @param templateId the ID of the template to fill
56	* @param componentId the ID of the component that will use this context
57	* @param targetNamespace the target namespace for the template, can be null to use the default namespace
58	*/
59	public TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace) {
60	this(contextType, templateId, componentId, targetNamespace, null);	21✔
61	}	3✔
62
63	/**
64	* Constructor for creating a new template context for filling a template.
65	*
66	* @param contextType the type of context
67	* @param templateId the ID of the template to fill
68	* @param componentId the ID of the component that will use this context
69	* @param existingNanopub an existing nanopub to fill, can be null if creating a new nanopub
70	*/
71	public TemplateContext(ContextType contextType, String templateId, String componentId, Nanopub existingNanopub) {
72	this(contextType, templateId, componentId, null, existingNanopub);	×
73	}	×
74
75	private TemplateContext(ContextType contextType, String templateId, String componentId, String targetNamespace, Nanopub existingNanopub) {	6✔
76	this.contextType = contextType;	9✔
77	// TODO: check whether template is of correct type:
78	this.template = TemplateData.get().getTemplate(templateId);	15✔
79	this.componentId = componentId;	9✔
80	if (targetNamespace != null) {	6✔
81	this.targetNamespace = targetNamespace;	9✔
82	}
83	this.existingNanopub = existingNanopub;	9✔
84	if (existingNanopub == null && NanodashSession.get().getUserIri() != null) {	15!
85	componentModels.put(NTEMPLATE.CREATOR_PLACEHOLDER, Model.of(NanodashSession.get().getUserIri().stringValue()));	×
86	}
87	}	3✔
88
89	/**
90	* Initializes the statements for this context.
91	*/
92	public void initStatements() {
93	if (statementItems != null) return;	9!
94	statementItems = new ArrayList<>();	15✔
95	for (IRI st : template.getStatementIris()) {	36✔
96	StatementItem si = new StatementItem(componentId, st, this);	24✔
97	statementItems.add(si);	15✔
98	for (IRI i : si.getIriSet()) {	33✔
99	if (iriSet.contains(i)) {	15✔
100	narrowScopeMap.remove(i);	18✔
101	} else {
102	iriSet.add(i);	15✔
103	narrowScopeMap.put(i, si);	18✔
104	}
105	}	3✔
106	}	3✔
107	}	3✔
108
109	/**
110	* Finalizes the statements by processing all parameters and setting the repetition counts.
111	*/
112	public void finalizeStatements() {
113	Map<StatementItem, Integer> finalRepetitionCount = new HashMap<>();	12✔
114	for (IRI ni : narrowScopeMap.keySet()) {	36✔
115	// TODO: Move all occurrences of this to utility function:
116	String postfix = Utils.getUriPostfix(ni);	9✔
117	StatementItem si = narrowScopeMap.get(ni);	18✔
118	int i = si.getRepetitionCount();	9✔
119	while (true) {
120	String p = postfix + "__" + i;	12✔
121	if (hasParam(p)) {	12!
122	si.addRepetitionGroup();	×
123	} else {
124	break;
125	}
126	i++;	×
127	}	×
128	i = 1;	6✔
129	int corr = 0;	6✔
130	if (si.isEmpty()) corr = 1;	15✔
131	while (true) {
132	String p = postfix + "__." + i;	12✔
133	if (hasParam(p)) {	12✔
134	int absPos = si.getRepetitionCount() + i - 1 - corr;	27✔
135	String param = postfix + "__" + absPos;	12✔
136	if (i - corr == 0) param = postfix;	12!
137	setParam(param, getParam(p));	18✔
138	finalRepetitionCount.put(si, i - corr);	24✔
139	} else {
140	break;
141	}
142	i++;	3✔
143	}	3✔
144	}	3✔
145	for (StatementItem si : finalRepetitionCount.keySet()) {	33✔
146	for (int i = 0; i < finalRepetitionCount.get(si); i++) {	33✔
147	si.addRepetitionGroup();	6✔
148	}
149	}	3✔
150	for (StatementItem si : statementItems) {	33✔
151	si.finalizeValues();	6✔
152	}	3✔
153	}	3✔
154
155	/**
156	* Sets the fill mode for this context.
157	*
158	* @param fillMode the fill mode to set
159	*/
160	public void setFillMode(FillMode fillMode) {
161	this.fillMode = fillMode;	9✔
162	}	3✔
163
164	/**
165	* Gets the fill mode for this context.
166	*
167	* @return the fill mode, or null if not set
168	*/
169	public FillMode getFillMode() {
170	return fillMode;	×
171	}
172
173	/**
174	* Returns the type of context.
175	*
176	* @return the context type
177	*/
178	public ContextType getType() {
179	return contextType;	×
180	}
181
182	/**
183	* Returns the template associated with this context.
184	*
185	* @return the template
186	*/
187	public Template getTemplate() {
188	return template;	9✔
189	}
190
191	/**
192	* Returns the ID of the template associated with this context.
193	*
194	* @return the template ID
195	*/
196	public String getTemplateId() {
197	return template.getId();	12✔
198	}
199
200	/**
201	* Sets a parameter for this context.
202	*
203	* @param name the name of the parameter
204	* @param value the value of the parameter
205	*/
206	public void setParam(String name, String value) {
207	params.put(name, value);	18✔
208	}	3✔
209
210	/**
211	* Gets a parameter value by its name.
212	*
213	* @param name the name of the parameter
214	* @return the value of the parameter, or null if not set
215	*/
216	public String getParam(String name) {
217	return params.get(name);	18✔
218	}
219
220	/**
221	* Checks if a parameter with the given name exists.
222	*
223	* @param name the name of the parameter
224	* @return true if the parameter exists, false otherwise
225	*/
226	public boolean hasParam(String name) {
227	return params.containsKey(name);	15✔
228	}
229
230	/**
231	* Returns the components associated with this context.
232	*
233	* @return a list of components
234	*/
235	public List<Component> getComponents() {
236	return components;	9✔
237	}
238
239	/**
240	* Returns the component models associated with this context.
241	*
242	* @return a map of IRI to model of strings
243	*/
244	public Map<IRI, IModel<?>> getComponentModels() {
245	return componentModels;	9✔
246	}
247
248	/**
249	* Returns the introduced IRIs in this context.
250	*
251	* @return a set of introduced IRIs
252	*/
253	public Set<IRI> getIntroducedIris() {
254	return introducedIris;	×
255	}
256
257	/**
258	* Returns the embedded IRIs in this context.
259	*
260	* @return a set of embedded IRIs
261	*/
262	public Set<IRI> getEmbeddedIris() {
263	return embeddedIris;	×
264	}
265
266	/**
267	* Processes an IRI by applying the template's processing rules.
268	*
269	* @param iri the IRI to process
270	* @return the processed IRI, or null if the processing results in no value
271	*/
272	public IRI processIri(IRI iri) {
273	Value v = processValue(iri);	12✔
274	if (v == null) return null;	6!
275	if (v instanceof IRI) return (IRI) v;	18!
276	return iri;	×
277	}
278
279	/**
280	* Processes a Value according to the template's rules.
281	*
282	* @param value the Value to process
283	* @return the processed Value, or the original Value if no processing is applicable
284	*/
285	public Value processValue(Value value) {
286	if (!(value instanceof IRI)) {	9!
287	return value;	×
288	}
289	IRI iri = (IRI) value;	9✔
290	if (iri.equals(NTEMPLATE.CREATOR_PLACEHOLDER)) {	12!
291	iri = NanodashSession.get().getUserIri();	×
292	}
293	if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {	12!
294	iri = vf.createIRI(targetNamespace + "assertion");	×
295	} else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {	12!
296	iri = vf.createIRI(targetNamespace);	×
297	} else if (template.isRootNanopubPlaceholder(iri)) {	15✔
298	IModel<?> rootModel = componentModels.get(iri);	18✔
299	String rootValue = (rootModel == null \|\| rootModel.getObject() == null) ? "" : rootModel.getObject().toString();	33!
300	if (rootValue.equals(LocalUri.of("nanopub").stringValue())) {	18✔
301	// Sentinel: in supersede/derive mode this means the existing nanopub was the root
302	Nanopub ref = getReferenceNanopub();	9✔
303	if (ref != null && (fillMode == FillMode.SUPERSEDE \|\| fillMode == FillMode.DERIVE)) {	18!
304	iri = vf.createIRI(ref.getUri().stringValue());	21✔
305	} else {
306	iri = vf.createIRI(targetNamespace);	15✔
307	}
308	} else if (rootValue.isEmpty()) {	12✔
309	iri = vf.createIRI(targetNamespace);	18✔
310	} else {
311	iri = vf.createIRI(rootValue);	12✔
312	}
313	}
314	// TODO: Move this code below to the respective placeholder classes:
315	IModel<?> tf = componentModels.get(iri);	18✔
316	Value processedValue = null;	6✔
317	Object tfObjectGeneric = null;	6✔
318	if (tf != null) {	6✔
319	tfObjectGeneric = tf.getObject();	9✔
320	}
321	if (template.isRestrictedChoicePlaceholder(iri)) {	15✔
322	String tfObject = (String) tfObjectGeneric;	9✔
323	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	21!
324	String prefix = template.getPrefix(iri);	15✔
325	if (prefix == null) prefix = "";	12!
326	if (template.isLocalResource(iri)) prefix = targetNamespace;	15!
327	if (tfObject.matches("https?://.+")) prefix = "";	12!
328	String v = prefix + tf.getObject();	18✔
329	if (v.matches("[^:# ]+")) v = targetNamespace + v;	27!
330	if (v.matches("https?://.*")) {	12!
331	processedValue = vf.createIRI(v);	15✔
332	} else {
333	processedValue = vf.createLiteral(tfObject);	×
334	}
335	}
336	} else if (template.isUriPlaceholder(iri)) {	18✔
337	String tfObject = (String) tfObjectGeneric;	9✔
338	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	21!
339	String prefix = template.getPrefix(iri);	15✔
340	if (prefix == null) prefix = "";	12!
341	if (template.isLocalResource(iri)) prefix = targetNamespace;	24✔
342	String v;
343	if (template.isAutoEscapePlaceholder(iri)) {	15!
344	v = prefix + Utils.urlEncode(tf.getObject());	×
345	} else {
346	if (tfObject.matches("https?://.+")) prefix = "";	18✔
347	v = prefix + tf.getObject();	18✔
348	}
349	if (v.matches("[^:# ]+")) v = targetNamespace + v;	12!
350	processedValue = vf.createIRI(v);	12✔
351	}
352	} else if (template.isLocalResource(iri)) {	18!
353	String tfObject = (String) tfObjectGeneric;	×
354	if (template.isIntroducedResource(iri) && fillMode == FillMode.SUPERSEDE) {	×
355	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	×
356	processedValue = vf.createIRI(tfObject);	×
357	}
358	} else {
359	String prefix = Utils.getUriPrefix(iri);	×
360	processedValue = vf.createIRI(iri.stringValue().replace(prefix, targetNamespace));	×
361	}
362	} else if (template.isLiteralPlaceholder(iri)) {	15✔
363	IRI datatype = template.getDatatype(iri);	15✔
364	String languageTag = template.getLanguageTag(iri);	15✔
365	if (datatype != null) {	6!
366	if (datatype.equals(XSD.DATETIME)) {	×
367	ZonedDateTime tfObject = (ZonedDateTime) tfObjectGeneric;	×
368	if (tfObject != null) {	×
369	processedValue = vf.createLiteral(tfObject);	×
370	}
371	} else if (datatype.equals(XSD.DATE)) {	×
372	Date tfObject = (Date) tfObjectGeneric;	×
373	if (tfObject != null) {	×
374	processedValue = vf.createLiteral(LiteralDateItem.format.format(tfObject), datatype);	×
375	}
376	}	×
377	} else {
378	String tfObject = (String) tfObjectGeneric;	9✔
379	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	21!
380	if (datatype != null) {	6!
381	processedValue = vf.createLiteral(tfObject, datatype);	×
382	} else if (languageTag != null) {	6!
383	processedValue = vf.createLiteral(tfObject, languageTag);	×
384	} else {
385	processedValue = vf.createLiteral(tfObject);	12✔
386	}
387	}
388	}
389	} else if (template.isValuePlaceholder(iri)) {	18!
390	String tfObject = (String) tfObjectGeneric;	×
391	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	×
392	if (Utils.isValidLiteralSerialization(tfObject)) {	×
393	processedValue = Utils.getParsedLiteral(tfObject);	×
394	} else {
395	String v = tfObject;	×
396	if (v.matches("[^:# ]+")) v = targetNamespace + v;	×
397	processedValue = vf.createIRI(v);	×
398	}
399	}
400	} else if (template.isSequenceElementPlaceholder(iri)) {	15!
401	String tfObject = (String) tfObjectGeneric;	×
402	if (tf != null && tfObject != null && !tfObject.isEmpty()) {	×
403	processedValue = vf.createIRI(tfObject);	×
404	}
405	} else {	×
406	processedValue = iri;	6✔
407	}
408	if (processedValue instanceof IRI pvIri && template.isIntroducedResource(iri)) {	33!
409	introducedIris.add(pvIri);	×
410	}
411	if (processedValue instanceof IRI pvIri && template.isEmbeddedResource(iri)) {	33!
412	embeddedIris.add(pvIri);	×
413	}
414	return processedValue;	6✔
415	}
416
417	/**
418	* Returns the statement items associated with this context.
419	*
420	* @return a list of StatementItem objects
421	*/
422	public List<StatementItem> getStatementItems() {
423	return statementItems;	×
424	}
425
426	/**
427	* Propagates the statements from this context to a NanopubCreator.
428	*
429	* @param npCreator the NanopubCreator to which the statements will be added
430	* @throws org.nanopub.MalformedNanopubException if there is an error in the nanopub structure
431	* @throws org.nanopub.NanopubAlreadyFinalizedException if the nanopub has already been finalized
432	*/
433	public void propagateStatements(NanopubCreator npCreator) throws MalformedNanopubException, NanopubAlreadyFinalizedException {
434	if (template.getNanopub() instanceof NanopubWithNs) {	×
435	NanopubWithNs np = (NanopubWithNs) template.getNanopub();	×
436	for (String p : np.getNsPrefixes()) {	×
437	npCreator.addNamespace(p, np.getNamespace(p));	×
438	}	×
439	}
440	for (StatementItem si : statementItems) {	×
441	si.addTriplesTo(npCreator);	×
442	}	×
443	}	×
444
445	/**
446	* Checks if the context has a narrow scope for the given IRI.
447	*
448	* @param iri the IRI to check
449	* @return true if there is a narrow scope for the IRI, false otherwise
450	*/
451	public boolean hasNarrowScope(IRI iri) {
452	return narrowScopeMap.containsKey(iri);	15✔
453	}
454
455	/**
456	* Checks if any of the statement items in this context will match any triple.
457	*
458	* @return true if any statement item will match any triple, false otherwise
459	*/
460	public boolean willMatchAnyTriple() {
461	initStatements();	×
462	for (StatementItem si : statementItems) {	×
463	if (si.willMatchAnyTriple()) return true;	×
464	}	×
465	return false;	×
466	}
467
468	/**
469	* Fills the context with statements, processing each StatementItem.
470	*
471	* @param statements the list of statements to fill
472	* @throws UnificationException if there is an error during unification of statements
473	*/
474	public void fill(List<Statement> statements) throws UnificationException {
475	for (StatementItem si : statementItems) {	33✔
476	// Isolate each statement: a unification failure on one must not abort the rest,
477	// otherwise every later template statement is left unmatched. Roll back any partial
478	// statement consumption so the next statement sees an intact pool.
479	List<Statement> statementsBefore = new ArrayList<>(statements);	15✔
480	try {
481	si.fill(statements);	9✔
482	} catch (UnificationException ex) {	×
483	logger.warn("Could not fill statement; continuing with the remaining statements", ex);	×
484	statements.clear();	×
485	statements.addAll(statementsBefore);	×
486	}	3✔
487	}	3✔
488	for (StatementItem si : statementItems) {	33✔
489	si.fillFinished();	6✔
490	}	3✔
491	}	3✔
492
493	/**
494	* Returns the existing Nanopub associated with this context, if any.
495	*
496	* @return the existing Nanopub, or null if this context is for a new Nanopub
497	*/
498	public Nanopub getExistingNanopub() {
499	return existingNanopub;	9✔
500	}
501
502	/**
503	* Returns the nanopub being used to fill this context (e.g. in supersede/derive
504	* mode), if any. Unlike {@link #getExistingNanopub()} this does not imply the
505	* context is read-only.
506	*
507	* @return the fill source nanopub, or null if none
508	*/
509	public Nanopub getFillSource() {
510	return fillSource;	9✔
511	}
512
513	/**
514	* Sets the nanopub used to fill this context (e.g. in supersede/derive mode).
515	*
516	* @param fillSource the nanopub providing the values, or null to clear
517	*/
518	public void setFillSource(Nanopub fillSource) {
519	this.fillSource = fillSource;	9✔
520	}	3✔
521
522	/**
523	* Returns the existing or fill-source nanopub for this context, preferring the
524	* existing nanopub if set.
525	*
526	* @return the reference nanopub, or null if none
527	*/
528	public Nanopub getReferenceNanopub() {
529	return existingNanopub != null ? existingNanopub : fillSource;	18!
530	}
531
532	/**
533	* Checks if this context is read-only.
534	*
535	* @return true if the context is read-only, false otherwise
536	*/
537	public boolean isReadOnly() {
538	return existingNanopub != null;	15!
539	}
540
541	/**
542	* Returns the label for a given IRI, if available.
543	*
544	* @param iri the IRI for which to get the label
545	* @return the label as a String, or null if no label is found
546	*/
547	public String getLabel(IRI iri) {
548	if (existingNanopub == null) return null;	×
549	if (labels == null) {	×
550	labels = new HashMap<>();	×
551	for (Statement st : existingNanopub.getPubinfo()) {	×
552	if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) \|\| st.getPredicate().equals(RDFS.LABEL)) {	×
553	String label = st.getObject().stringValue();	×
554	labels.put((IRI) st.getSubject(), label);	×
555	}
556	}	×
557	}
558	return labels.get(iri);	×
559	}
560
561	}

knowledgepixels / nanodash / 28111182502

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