16989716008

Committed 15 Aug 2025 12:12PM UTC coverage: 25.926% (+0.1%) from 25.779%

Build # 16989716008

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: update code style and files formatting

Run Details

122 of 494 branches covered (24.7%)

Branch coverage included in aggregate %.

333 of 1261 relevant lines covered (26.41%)

1.29 hits per line

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81.75

src/main/java/com/knowledgepixels/query/OpenApiSpecPage.java

package com.knowledgepixels.query;

import io.vertx.core.MultiMap;
import net.trustyuri.TrustyUriUtils;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.eclipse.rdf4j.query.algebra.Var;
import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
import org.eclipse.rdf4j.query.parser.ParsedQuery;
import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
import org.nanopub.Nanopub;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.extra.services.QueryAccess;
import org.yaml.snakeyaml.DumperOptions;
import org.yaml.snakeyaml.Yaml;

import java.util.*;

/**
 * Page for Open API compliant specification.
 */
public class OpenApiSpecPage {

    private Map<String, Object> dataMap = new LinkedHashMap<>();
    private Nanopub np;

    /**
     * Creates a new page instance.
     *
     * @param requestUrl The request URL
     * @param parameters The URL request parameters
     */
    public OpenApiSpecPage(String requestUrl, MultiMap parameters) {
        requestUrl = requestUrl.replaceFirst("\\?.*$", "");
        if (!requestUrl.matches(".*/RA[A-Za-z0-9\\-_]{43}/(.*)?")) return;
        String artifactCode = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$2");
//                String queryPart = requestUrl.replaceFirst("^(.*/)(RA[A-Za-z0-9\\-_]{43}/)(.*)?$", "$3");
//                String requestUrlBase = requestUrl.replaceFirst("^/(.*/)(RA[A-Za-z0-9\\-_]{43})/(.*)?$", "$1");

        // TODO Get the nanopub from the local store:
        np = GetNanopub.get(artifactCode);
        if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {
            // TODO Get the latest version from the local store:
            np = GetNanopub.get(QueryAccess.getLatestVersionId(np.getUri().stringValue()));
            artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());
        }
        String queryName = null;
        String label = null;
        String desc = null;
        String queryContent = null;
        String endpoint = null;
        for (Statement st : np.getAssertion()) {
            if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) continue;
            String qn = st.getSubject().stringValue().replaceFirst("^.*[#/](.*)$", "$1");
            if (queryName != null && !qn.equals(queryName)) {
                np = null;
                break;
            }
            queryName = qn;
            if (st.getPredicate().equals(RDFS.LABEL)) {
                label = st.getObject().stringValue();
            } else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {
                desc = st.getObject().stringValue();
//                        } else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {
//                                license = st.getObject().stringValue();
            } else if (st.getPredicate().equals(GrlcSpecPage.HAS_SPARQL)) {
                queryContent = st.getObject().stringValue().replace("https://w3id.org/np/l/nanopub-query-1.1/", GrlcSpecPage.nanopubQueryUrl);
            } else if (st.getPredicate().equals(GrlcSpecPage.HAS_ENDPOINT) && st.getObject() instanceof IRI) {
                endpoint = st.getObject().stringValue();
                if (endpoint.startsWith("https://w3id.org/np/l/nanopub-query-1.1/")) {
                    endpoint = endpoint.replace("https://w3id.org/np/l/nanopub-query-1.1/", GrlcSpecPage.nanopubQueryUrl);
                }
            }
        }

        // TODO Code duplicated from com.knowledgepixels.nanodash.GrlcQuery:
        final Set<String> placeholders = new HashSet<>();
        ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);
        query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {

            @Override
            public void meet(Var node) throws RuntimeException {
                super.meet(node);
                if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {
                    placeholders.add(node.getName());
                }
            }

        });
        List<String> placeholdersList = new ArrayList<>(placeholders);
        Collections.sort(placeholdersList);

        dataMap.put("openapi", "3.0.4");

        Map<String, Object> infoMap = new LinkedHashMap<>();
        infoMap.put("title", label);
        infoMap.put("description", "API definition source: <a target=\"_blank\" href=\"" + np.getUri() + "\"><svg height=\"0.8em\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 8 8\"><path d=\"M5,8H8L3,0H0M8,4.8V0H5M0,3.2V8H3\"/></svg> " + artifactCode.substring(0, 10) + "</a>");
        infoMap.put("version", artifactCode.substring(0, 10));
        dataMap.put("info", infoMap);

        List<Object> serversList = new ArrayList<>();
        Map<String, Object> serverMap = new LinkedHashMap<>();
        serverMap.put("url", Utils.getEnvString("NANOPUB_QUERY_URL", "http://localhost:9393/") + "api/" + artifactCode);
        serverMap.put("description", "This Nanopub Query instance");
        serversList.add(serverMap);
        dataMap.put("servers", serversList);

        Map<String, Object> pathsMap = new LinkedHashMap<>();
        Map<String, Object> rootPathMap = new LinkedHashMap<>();
        Map<String, Object> getOpMap = new LinkedHashMap<>();
        //getOpMap.put("summary", label);
        getOpMap.put("description", desc);
        Map<String, Object> responsesMap = new LinkedHashMap<>();
        Map<String, Object> successrespMap = new LinkedHashMap<>();
        Map<String, Object> contentMap = new LinkedHashMap<>();
        contentMap.put("text/csv", new HashMap<>());
        contentMap.put("application/json", new HashMap<>());
        successrespMap.put("content", contentMap);
        successrespMap.put("description", "result table");
        responsesMap.put("200", successrespMap);
        List<Object> parametersList = new ArrayList<>();
        for (String p : placeholdersList) {
            Map<String, Object> paramMap = new LinkedHashMap<>();
            paramMap.put("in", "query");
            String name = p.replaceFirst("^_*", "").replaceFirst("_iri$", "");
            paramMap.put("name", name);
            paramMap.put("required", !p.startsWith("__"));
            Map<String, Object> stringType = new LinkedHashMap<>();
            stringType.put("type", "string");
            paramMap.put("schema", stringType);
            parametersList.add(paramMap);
        }
        getOpMap.put("parameters", parametersList);
        getOpMap.put("responses", responsesMap);
        rootPathMap.put("get", getOpMap);
        pathsMap.put("/" + queryName, rootPathMap);
        dataMap.put("paths", pathsMap);
    }

    /**
     * Returns the Open API spec as a string.
     *
     * @return Open API specification string
     */
    public String getSpec() {
        if (np == null) return null;
        final DumperOptions options = new DumperOptions();
        options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK);
        options.setPrettyFlow(true);
        return new Yaml(options).dump(dataMap);
    }

}

1	package com.knowledgepixels.query;
2
3	import io.vertx.core.MultiMap;
4	import net.trustyuri.TrustyUriUtils;
5	import org.eclipse.rdf4j.model.IRI;
6	import org.eclipse.rdf4j.model.Statement;
7	import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
8	import org.eclipse.rdf4j.model.vocabulary.RDFS;
9	import org.eclipse.rdf4j.query.algebra.Var;
10	import org.eclipse.rdf4j.query.algebra.helpers.AbstractSimpleQueryModelVisitor;
11	import org.eclipse.rdf4j.query.parser.ParsedQuery;
12	import org.eclipse.rdf4j.query.parser.sparql.SPARQLParser;
13	import org.nanopub.Nanopub;
14	import org.nanopub.extra.server.GetNanopub;
15	import org.nanopub.extra.services.QueryAccess;
16	import org.yaml.snakeyaml.DumperOptions;
17	import org.yaml.snakeyaml.Yaml;
18
19	import java.util.*;
20
21	/**
22	* Page for Open API compliant specification.
23	*/
24	public class OpenApiSpecPage {
25
26	private Map<String, Object> dataMap = new LinkedHashMap<>();	5✔
27	private Nanopub np;
28
29	/**
30	* Creates a new page instance.
31	*
32	* @param requestUrl The request URL
33	* @param parameters The URL request parameters
34	*/
35	public OpenApiSpecPage(String requestUrl, MultiMap parameters) {	2✔
36	requestUrl = requestUrl.replaceFirst("\\?.*$", "");	5✔
37	if (!requestUrl.matches("./RA[A-Za-z0-9\\-_]{43}/(.)?")) return;	5✔
38	String artifactCode = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$2");	5✔
39	// String queryPart = requestUrl.replaceFirst("^(./)(RA[A-Za-z0-9\\-_]{43}/)(.)?$", "$3");
40	// String requestUrlBase = requestUrl.replaceFirst("^/(./)(RA[A-Za-z0-9\\-_]{43})/(.)?$", "$1");
41
42	// TODO Get the nanopub from the local store:
43	np = GetNanopub.get(artifactCode);	4✔
44	if (parameters.get("api-version") != null && parameters.get("api-version").equals("latest")) {	10!
45	// TODO Get the latest version from the local store:
46	np = GetNanopub.get(QueryAccess.getLatestVersionId(np.getUri().stringValue()));	8✔
47	artifactCode = TrustyUriUtils.getArtifactCode(np.getUri().stringValue());	6✔
48	}
49	String queryName = null;	2✔
50	String label = null;	2✔
51	String desc = null;	2✔
52	String queryContent = null;	2✔
53	String endpoint = null;	2✔
54	for (Statement st : np.getAssertion()) {	12✔
55	if (!st.getSubject().stringValue().startsWith(np.getUri().stringValue())) continue;	9!
56	String qn = st.getSubject().stringValue().replaceFirst("^.[#/](.)$", "$1");	7✔
57	if (queryName != null && !qn.equals(queryName)) {	6!
58	np = null;	×
59	break;	×
60	}
61	queryName = qn;	2✔
62	if (st.getPredicate().equals(RDFS.LABEL)) {	5✔
63	label = st.getObject().stringValue();	5✔
64	} else if (st.getPredicate().equals(DCTERMS.DESCRIPTION)) {	5✔
65	desc = st.getObject().stringValue();	5✔
66	// } else if (st.getPredicate().equals(DCTERMS.LICENSE) && st.getObject() instanceof IRI) {
67	// license = st.getObject().stringValue();
68	} else if (st.getPredicate().equals(GrlcSpecPage.HAS_SPARQL)) {	5✔
69	queryContent = st.getObject().stringValue().replace("https://w3id.org/np/l/nanopub-query-1.1/", GrlcSpecPage.nanopubQueryUrl);	8✔
70	} else if (st.getPredicate().equals(GrlcSpecPage.HAS_ENDPOINT) && st.getObject() instanceof IRI) {	9!
71	endpoint = st.getObject().stringValue();	4✔
72	if (endpoint.startsWith("https://w3id.org/np/l/nanopub-query-1.1/")) {	4!
73	endpoint = endpoint.replace("https://w3id.org/np/l/nanopub-query-1.1/", GrlcSpecPage.nanopubQueryUrl);	5✔
74	}
75	}
76	}	1✔
77
78	// TODO Code duplicated from com.knowledgepixels.nanodash.GrlcQuery:
79	final Set<String> placeholders = new HashSet<>();	4✔
80	ParsedQuery query = new SPARQLParser().parseQuery(queryContent, null);	7✔
81	query.getTupleExpr().visitChildren(new AbstractSimpleQueryModelVisitor<>() {	14✔
82
83	@Override
84	public void meet(Var node) throws RuntimeException {
85	super.meet(node);	3✔
86	if (!node.isConstant() && !node.isAnonymous() && node.getName().startsWith("_")) {	11!
87	placeholders.add(node.getName());	×
88	}
89	}	1✔
90
91	});
92	List<String> placeholdersList = new ArrayList<>(placeholders);	5✔
93	Collections.sort(placeholdersList);	2✔
94
95	dataMap.put("openapi", "3.0.4");	6✔
96
97	Map<String, Object> infoMap = new LinkedHashMap<>();	4✔
98	infoMap.put("title", label);	5✔
99	infoMap.put("description", "API definition source: <a target=\"_blank\" href=\"" + np.getUri() + "\"><svg height=\"0.8em\" xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 8 8\"><path d=\"M5,8H8L3,0H0M8,4.8V0H5M0,3.2V8H3\"/></svg> " + artifactCode.substring(0, 10) + "</a>");	13✔
100	infoMap.put("version", artifactCode.substring(0, 10));	8✔
101	dataMap.put("info", infoMap);	6✔
102
103	List<Object> serversList = new ArrayList<>();	4✔
104	Map<String, Object> serverMap = new LinkedHashMap<>();	4✔
105	serverMap.put("url", Utils.getEnvString("NANOPUB_QUERY_URL", "http://localhost:9393/") + "api/" + artifactCode);	9✔
106	serverMap.put("description", "This Nanopub Query instance");	5✔
107	serversList.add(serverMap);	4✔
108	dataMap.put("servers", serversList);	6✔
109
110	Map<String, Object> pathsMap = new LinkedHashMap<>();	4✔
111	Map<String, Object> rootPathMap = new LinkedHashMap<>();	4✔
112	Map<String, Object> getOpMap = new LinkedHashMap<>();	4✔
113	//getOpMap.put("summary", label);
114	getOpMap.put("description", desc);	5✔
115	Map<String, Object> responsesMap = new LinkedHashMap<>();	4✔
116	Map<String, Object> successrespMap = new LinkedHashMap<>();	4✔
117	Map<String, Object> contentMap = new LinkedHashMap<>();	4✔
118	contentMap.put("text/csv", new HashMap<>());	7✔
119	contentMap.put("application/json", new HashMap<>());	7✔
120	successrespMap.put("content", contentMap);	5✔
121	successrespMap.put("description", "result table");	5✔
122	responsesMap.put("200", successrespMap);	5✔
123	List<Object> parametersList = new ArrayList<>();	4✔
124	for (String p : placeholdersList) {	6!
125	Map<String, Object> paramMap = new LinkedHashMap<>();	×
126	paramMap.put("in", "query");	×
127	String name = p.replaceFirst("^_*", "").replaceFirst("_iri$", "");	×
128	paramMap.put("name", name);	×
129	paramMap.put("required", !p.startsWith("__"));	×
130	Map<String, Object> stringType = new LinkedHashMap<>();	×
131	stringType.put("type", "string");	×
132	paramMap.put("schema", stringType);	×
133	parametersList.add(paramMap);	×
134	}	×
135	getOpMap.put("parameters", parametersList);	5✔
136	getOpMap.put("responses", responsesMap);	5✔
137	rootPathMap.put("get", getOpMap);	5✔
138	pathsMap.put("/" + queryName, rootPathMap);	6✔
139	dataMap.put("paths", pathsMap);	6✔
140	}	1✔
141
142	/**
143	* Returns the Open API spec as a string.
144	*
145	* @return Open API specification string
146	*/
147	public String getSpec() {
148	if (np == null) return null;	5✔
149	final DumperOptions options = new DumperOptions();	4✔
150	options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK);	3✔
151	options.setPrettyFlow(true);	3✔
152	return new Yaml(options).dump(dataMap);	8✔
153	}
154
155	}

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