20374513260

Committed 19 Dec 2025 03:27PM UTC coverage: 0.954% (-0.2%) from 1.118%

Build # 20374513260

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: update NanopubLoader and Utils to use NPX vocabulary

Run Details

6 of 592 branches covered (1.01%)

Branch coverage included in aggregate %.

17 of 1819 relevant lines covered (0.93%)

0.11 hits per line

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14.38

src/main/java/com/knowledgepixels/registry/Utils.java

package com.knowledgepixels.registry;

import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
import com.github.jsonldjava.shaded.com.google.common.reflect.TypeToken;
import com.google.common.hash.Hashing;
import com.google.gson.Gson;
import com.google.gson.JsonIOException;
import com.google.gson.JsonSyntaxException;
import com.mongodb.client.ClientSession;
import io.vertx.ext.web.RoutingContext;
import net.trustyuri.TrustyUriUtils;
import org.apache.commons.lang.StringUtils;
import org.commonjava.mimeparse.MIMEParse;
import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.NanopubUtils;
import org.nanopub.extra.setting.NanopubSetting;
import org.nanopub.vocabulary.NPX;

import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.lang.reflect.Type;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
import java.util.*;

public class Utils {

    private Utils() {
    }  // no instances allowed

    public static String getMimeType(RoutingContext context, String supported) {
        List<String> supportedList = Arrays.asList(StringUtils.split(supported, ','));
        String mimeType = supportedList.get(0);
        try {
            mimeType = MIMEParse.bestMatch(supportedList, context.request().getHeader("Accept"));
        } catch (Exception ex) {
        }
        return mimeType;
    }

    public static String urlEncode(Object o) {
        try {
            return URLEncoder.encode((o == null ? "" : o.toString()), "UTF-8");
        } catch (UnsupportedEncodingException ex) {
            throw new RuntimeException(ex);
        }
    }

    public static String getHash(String s) {
        return Hashing.sha256().hashString(s, Charsets.UTF_8).toString();
    }

    public static Set<IRI> getInvalidatedNanopubIds(Nanopub np) {
        Set<IRI> l = new HashSet<IRI>();
        for (Statement st : NanopubUtils.getStatements(np)) {
            if (!(st.getObject() instanceof IRI)) continue;
            Resource s = st.getSubject();
            IRI p = st.getPredicate();
            if ((p.equals(NPX.RETRACTS) || p.equals(NPX.INVALIDATES)) || (p.equals(NPX.SUPERSEDES) && s.equals(np.getUri()))) {
                if (TrustyUriUtils.isPotentialTrustyUri(st.getObject().stringValue())) {
                    l.add((IRI) st.getObject());
                }
            }
        }
        return l;
    }

    public static String getEnv(String name, String defaultValue) {
        String value = System.getenv(name);
        if (value == null) value = defaultValue;
        return value;
    }

    public static String getTypeHash(ClientSession mongoSession, Object type) {
        String typeHash = Utils.getHash(type.toString());
        if (type.toString().equals("$")) {
            typeHash = "$";
        } else {
            RegistryDB.recordHash(mongoSession, type.toString());
        }
        return typeHash;
    }

    public static String getAgentLabel(String agentId) {
        if (agentId == null || agentId.isBlank()) {
            throw new IllegalArgumentException("Agent ID cannot be null or blank");
        }
        agentId = agentId.replaceFirst("^https://orcid\\.org/", "orcid:");
        if (agentId.length() > 55) {
            return agentId.substring(0, 50) + "...";
        }
        return agentId;
    }

    public static boolean isUnloadedStatus(String status) {
        if (status.equals("seen")) return true;  // only exists in "accounts_loading"?
        if (status.equals("skipped")) return true;
        return false;
    }

    public static boolean isCoreLoadedStatus(String status) {
        if (status.equals("visited")) return true;  // only exists in "accounts_loading"?
        if (status.equals("expanded")) return true;  // only exists in "accounts_loading"?
        if (status.equals("processed")) return true;  // only exists in "accounts_loading"?
        if (status.equals("aggregated")) return true;  // only exists in "accounts_loading"?
        if (status.equals("approved")) return true;  // only exists in "accounts_loading"?
        if (status.equals("contested")) return true;
        if (status.equals("toLoad")) return true;  // only exists in "accounts_loading"?
        if (status.equals("loaded")) return true;
        return false;
    }

    public static boolean isFullyLoadedStatus(String status) {
        if (status.equals("loaded")) return true;
        return false;
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();
    public static final IRI APPROVES_OF = vf.createIRI("http://purl.org/nanopub/x/approvesOf");

    public static final IRI APPROVAL_TYPE = vf.createIRI("http://purl.org/nanopub/x/approvesOf");

    public static final String TYPE_JSON = "application/json";
    public static final String TYPE_TRIG = "application/trig";
    public static final String TYPE_JELLY = "application/x-jelly-rdf";
    public static final String TYPE_JSONLD = "application/ld+json";
    public static final String TYPE_NQUADS = "application/n-quads";
    public static final String TYPE_TRIX = "application/trix";
    public static final String TYPE_HTML = "text/html";

    // Content types supported on a ListPage
    public static final String SUPPORTED_TYPES_LIST = TYPE_JSON + "," + TYPE_JELLY + "," + TYPE_HTML;
    // Content types supported on a NanopubPage
    public static final String SUPPORTED_TYPES_NANOPUB = TYPE_TRIG + "," + TYPE_JELLY + "," + TYPE_JSONLD + "," + TYPE_NQUADS + "," + TYPE_TRIX + "," + TYPE_HTML;

    private static Map<String, String> extensionTypeMap;

    public static String getType(String extension) {
        if (extension == null) {
            return null;
        }
        if (extensionTypeMap == null) {
            extensionTypeMap = new HashMap<>();
            extensionTypeMap.put("trig", TYPE_TRIG);
            extensionTypeMap.put("jelly", TYPE_JELLY);
            extensionTypeMap.put("jsonld", TYPE_JSONLD);
            extensionTypeMap.put("nq", TYPE_NQUADS);
            extensionTypeMap.put("xml", TYPE_TRIX);
            extensionTypeMap.put("html", TYPE_HTML);
            extensionTypeMap.put("json", TYPE_JSON);
        }
        return extensionTypeMap.get(extension);
    }

    private static List<String> peerUrls;

    public static List<String> getPeerUrls() {
        if (peerUrls == null) {
            String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");
            String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");
            if (!envPeerUrls.isEmpty()) {
                peerUrls = new ArrayList<>();
                for (String peerUrl : envPeerUrls.split(";")) {
                    if (thisRegistryUrl.equals(peerUrl)) continue;
                    peerUrls.add(peerUrl);
                }
            } else {
                NanopubSetting setting;
                try {
                    setting = getSetting();
                } catch (Exception ex) {
                    throw new RuntimeException(ex);
                }
                peerUrls = new ArrayList<>();
                for (IRI iri : setting.getBootstrapServices()) {
                    String peerUrl = iri.stringValue();
                    if (thisRegistryUrl.equals(peerUrl)) continue;
                    peerUrls.add(peerUrl);
                }
            }
        }
        return peerUrls;
    }

    private static final String SETTING_FILE_PATH = Utils.getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");
    private static NanopubSetting settingNp;

    public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
        if (settingNp == null) {
            settingNp = new NanopubSetting(new NanopubImpl(new File(SETTING_FILE_PATH)));
        }
        return settingNp;
    }

    public static String getRandomPeer() throws RDF4JException, MalformedNanopubException, IOException {
        List<String> peerUrls = getPeerUrls();
        return peerUrls.get(random.nextInt(peerUrls.size()));
    }

    private static Random random = new Random();

    public static Random getRandom() {
        return random;
    }

    private static Gson g = new Gson();
    private static Type listType = new TypeToken<List<String>>() {
    }.getType();

    public static List<String> retrieveListFromJsonUrl(String url) throws JsonIOException, JsonSyntaxException, MalformedURLException, IOException {
        return g.fromJson(new InputStreamReader(new URL(url).openStream()), listType);
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
4	import com.github.jsonldjava.shaded.com.google.common.reflect.TypeToken;
5	import com.google.common.hash.Hashing;
6	import com.google.gson.Gson;
7	import com.google.gson.JsonIOException;
8	import com.google.gson.JsonSyntaxException;
9	import com.mongodb.client.ClientSession;
10	import io.vertx.ext.web.RoutingContext;
11	import net.trustyuri.TrustyUriUtils;
12	import org.apache.commons.lang.StringUtils;
13	import org.commonjava.mimeparse.MIMEParse;
14	import org.eclipse.rdf4j.common.exception.RDF4JException;
15	import org.eclipse.rdf4j.model.IRI;
16	import org.eclipse.rdf4j.model.Resource;
17	import org.eclipse.rdf4j.model.Statement;
18	import org.eclipse.rdf4j.model.ValueFactory;
19	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
20	import org.nanopub.MalformedNanopubException;
21	import org.nanopub.Nanopub;
22	import org.nanopub.NanopubImpl;
23	import org.nanopub.NanopubUtils;
24	import org.nanopub.extra.setting.NanopubSetting;
25	import org.nanopub.vocabulary.NPX;
26
27	import java.io.File;
28	import java.io.IOException;
29	import java.io.InputStreamReader;
30	import java.io.UnsupportedEncodingException;
31	import java.lang.reflect.Type;
32	import java.net.MalformedURLException;
33	import java.net.URL;
34	import java.net.URLEncoder;
35	import java.util.*;
36
37	public class Utils {
38
39	private Utils() {
40	} // no instances allowed
41
42	public static String getMimeType(RoutingContext context, String supported) {
43	List<String> supportedList = Arrays.asList(StringUtils.split(supported, ','));	×
44	String mimeType = supportedList.get(0);	×
45	try {
46	mimeType = MIMEParse.bestMatch(supportedList, context.request().getHeader("Accept"));	×
47	} catch (Exception ex) {	×
48	}	×
49	return mimeType;	×
50	}
51
52	public static String urlEncode(Object o) {
53	try {
54	return URLEncoder.encode((o == null ? "" : o.toString()), "UTF-8");	×
55	} catch (UnsupportedEncodingException ex) {	×
56	throw new RuntimeException(ex);	×
57	}
58	}
59
60	public static String getHash(String s) {
61	return Hashing.sha256().hashString(s, Charsets.UTF_8).toString();	18✔
62	}
63
64	public static Set<IRI> getInvalidatedNanopubIds(Nanopub np) {
65	Set<IRI> l = new HashSet<IRI>();	×
66	for (Statement st : NanopubUtils.getStatements(np)) {	×
67	if (!(st.getObject() instanceof IRI)) continue;	×
68	Resource s = st.getSubject();	×
69	IRI p = st.getPredicate();	×
70	if ((p.equals(NPX.RETRACTS) \|\| p.equals(NPX.INVALIDATES)) \|\| (p.equals(NPX.SUPERSEDES) && s.equals(np.getUri()))) {	×
71	if (TrustyUriUtils.isPotentialTrustyUri(st.getObject().stringValue())) {	×
72	l.add((IRI) st.getObject());	×
73	}
74	}
75	}	×
76	return l;	×
77	}
78
79	public static String getEnv(String name, String defaultValue) {
80	String value = System.getenv(name);	9✔
81	if (value == null) value = defaultValue;	12!
82	return value;	6✔
83	}
84
85	public static String getTypeHash(ClientSession mongoSession, Object type) {
86	String typeHash = Utils.getHash(type.toString());	×
87	if (type.toString().equals("$")) {	×
88	typeHash = "$";	×
89	} else {
90	RegistryDB.recordHash(mongoSession, type.toString());	×
91	}
92	return typeHash;	×
93	}
94
95	public static String getAgentLabel(String agentId) {
96	if (agentId == null \|\| agentId.isBlank()) {	15✔
97	throw new IllegalArgumentException("Agent ID cannot be null or blank");	15✔
98	}
99	agentId = agentId.replaceFirst("^https://orcid\\.org/", "orcid:");	15✔
100	if (agentId.length() > 55) {	12!
101	return agentId.substring(0, 50) + "...";	×
102	}
103	return agentId;	6✔
104	}
105
106	public static boolean isUnloadedStatus(String status) {
107	if (status.equals("seen")) return true; // only exists in "accounts_loading"?	×
108	if (status.equals("skipped")) return true;	×
109	return false;	×
110	}
111
112	public static boolean isCoreLoadedStatus(String status) {
113	if (status.equals("visited")) return true; // only exists in "accounts_loading"?	×
114	if (status.equals("expanded")) return true; // only exists in "accounts_loading"?	×
115	if (status.equals("processed")) return true; // only exists in "accounts_loading"?	×
116	if (status.equals("aggregated")) return true; // only exists in "accounts_loading"?	×
117	if (status.equals("approved")) return true; // only exists in "accounts_loading"?	×
118	if (status.equals("contested")) return true;	×
119	if (status.equals("toLoad")) return true; // only exists in "accounts_loading"?	×
120	if (status.equals("loaded")) return true;	×
121	return false;	×
122	}
123
124	public static boolean isFullyLoadedStatus(String status) {
125	if (status.equals("loaded")) return true;	×
126	return false;	×
127	}
128
129	private static ValueFactory vf = SimpleValueFactory.getInstance();	6✔
130	public static final IRI APPROVES_OF = vf.createIRI("http://purl.org/nanopub/x/approvesOf");	12✔
131
132	public static final IRI APPROVAL_TYPE = vf.createIRI("http://purl.org/nanopub/x/approvesOf");	12✔
133
134	public static final String TYPE_JSON = "application/json";
135	public static final String TYPE_TRIG = "application/trig";
136	public static final String TYPE_JELLY = "application/x-jelly-rdf";
137	public static final String TYPE_JSONLD = "application/ld+json";
138	public static final String TYPE_NQUADS = "application/n-quads";
139	public static final String TYPE_TRIX = "application/trix";
140	public static final String TYPE_HTML = "text/html";
141
142	// Content types supported on a ListPage
143	public static final String SUPPORTED_TYPES_LIST = TYPE_JSON + "," + TYPE_JELLY + "," + TYPE_HTML;
144	// Content types supported on a NanopubPage
145	public static final String SUPPORTED_TYPES_NANOPUB = TYPE_TRIG + "," + TYPE_JELLY + "," + TYPE_JSONLD + "," + TYPE_NQUADS + "," + TYPE_TRIX + "," + TYPE_HTML;
146
147	private static Map<String, String> extensionTypeMap;
148
149	public static String getType(String extension) {
150	if (extension == null) {	×
151	return null;	×
152	}
153	if (extensionTypeMap == null) {	×
154	extensionTypeMap = new HashMap<>();	×
155	extensionTypeMap.put("trig", TYPE_TRIG);	×
156	extensionTypeMap.put("jelly", TYPE_JELLY);	×
157	extensionTypeMap.put("jsonld", TYPE_JSONLD);	×
158	extensionTypeMap.put("nq", TYPE_NQUADS);	×
159	extensionTypeMap.put("xml", TYPE_TRIX);	×
160	extensionTypeMap.put("html", TYPE_HTML);	×
161	extensionTypeMap.put("json", TYPE_JSON);	×
162	}
163	return extensionTypeMap.get(extension);	×
164	}
165
166	private static List<String> peerUrls;
167
168	public static List<String> getPeerUrls() {
169	if (peerUrls == null) {	×
170	String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");	×
171	String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");	×
172	if (!envPeerUrls.isEmpty()) {	×
173	peerUrls = new ArrayList<>();	×
174	for (String peerUrl : envPeerUrls.split(";")) {	×
175	if (thisRegistryUrl.equals(peerUrl)) continue;	×
176	peerUrls.add(peerUrl);	×
177	}
178	} else {
179	NanopubSetting setting;
180	try {
181	setting = getSetting();	×
182	} catch (Exception ex) {	×
183	throw new RuntimeException(ex);	×
184	}	×
185	peerUrls = new ArrayList<>();	×
186	for (IRI iri : setting.getBootstrapServices()) {	×
187	String peerUrl = iri.stringValue();	×
188	if (thisRegistryUrl.equals(peerUrl)) continue;	×
189	peerUrls.add(peerUrl);	×
190	}	×
191	}
192	}
193	return peerUrls;	×
194	}
195
196	private static final String SETTING_FILE_PATH = Utils.getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");	12✔
197	private static NanopubSetting settingNp;
198
199	public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
200	if (settingNp == null) {	×
201	settingNp = new NanopubSetting(new NanopubImpl(new File(SETTING_FILE_PATH)));	×
202	}
203	return settingNp;	×
204	}
205
206	public static String getRandomPeer() throws RDF4JException, MalformedNanopubException, IOException {
207	List<String> peerUrls = getPeerUrls();	×
208	return peerUrls.get(random.nextInt(peerUrls.size()));	×
209	}
210
211	private static Random random = new Random();	12✔
212
213	public static Random getRandom() {
214	return random;	×
215	}
216
217	private static Gson g = new Gson();	12✔
218	private static Type listType = new TypeToken<List<String>>() {	21✔
219	}.getType();	6✔
220
221	public static List<String> retrieveListFromJsonUrl(String url) throws JsonIOException, JsonSyntaxException, MalformedURLException, IOException {
222	return g.fromJson(new InputStreamReader(new URL(url).openStream()), listType);	×
223	}
224
225	}

knowledgepixels / nanopub-registry / 20374513260

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