20413250445

Committed 21 Dec 2025 05:19PM UTC coverage: 0.924% (-0.03%) from 0.954%

Build # 20413250445

Build Type

push

github

Committed by

ashleycaselli

Commit Message

chore: minor code cleanup

Run Details

6 of 592 branches covered (1.01%)

Branch coverage included in aggregate %.

16 of 1789 relevant lines covered (0.89%)

0.11 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

14.01

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.lang.reflect.Type;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
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.getFirst();
        try {
            mimeType = MIMEParse.bestMatch(supportedList, context.request().getHeader("Accept"));
        } catch (Exception ex) {
        }
        return mimeType;
    }

    public static String urlEncode(Object o) {
        return URLEncoder.encode((o == null ? "" : o.toString()), StandardCharsets.UTF_8);
    }

    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 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 {
        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, IOException, URISyntaxException {
        return g.fromJson(new InputStreamReader(new URI(url).toURL().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.lang.reflect.Type;
31	import java.net.URI;
32	import java.net.URISyntaxException;
33	import java.net.URLEncoder;
34	import java.nio.charset.StandardCharsets;
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.getFirst();	×
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	return URLEncoder.encode((o == null ? "" : o.toString()), StandardCharsets.UTF_8);	×
54	}
55
56	public static String getHash(String s) {
57	return Hashing.sha256().hashString(s, Charsets.UTF_8).toString();	18✔
58	}
59
60	public static Set<IRI> getInvalidatedNanopubIds(Nanopub np) {
61	Set<IRI> l = new HashSet<IRI>();	×
62	for (Statement st : NanopubUtils.getStatements(np)) {	×
63	if (!(st.getObject() instanceof IRI)) continue;	×
64	Resource s = st.getSubject();	×
65	IRI p = st.getPredicate();	×
66	if ((p.equals(NPX.RETRACTS) \|\| p.equals(NPX.INVALIDATES)) \|\| (p.equals(NPX.SUPERSEDES) && s.equals(np.getUri()))) {	×
67	if (TrustyUriUtils.isPotentialTrustyUri(st.getObject().stringValue())) {	×
68	l.add((IRI) st.getObject());	×
69	}
70	}
71	}	×
72	return l;	×
73	}
74
75	public static String getEnv(String name, String defaultValue) {
76	String value = System.getenv(name);	9✔
77	if (value == null) value = defaultValue;	12!
78	return value;	6✔
79	}
80
81	public static String getTypeHash(ClientSession mongoSession, Object type) {
82	String typeHash = Utils.getHash(type.toString());	×
83	if (type.toString().equals("$")) {	×
84	typeHash = "$";	×
85	} else {
86	RegistryDB.recordHash(mongoSession, type.toString());	×
87	}
88	return typeHash;	×
89	}
90
91	public static String getAgentLabel(String agentId) {
92	if (agentId == null \|\| agentId.isBlank()) {	15✔
93	throw new IllegalArgumentException("Agent ID cannot be null or blank");	15✔
94	}
95	agentId = agentId.replaceFirst("^https://orcid\\.org/", "orcid:");	15✔
96	if (agentId.length() > 55) {	12!
97	return agentId.substring(0, 50) + "...";	×
98	}
99	return agentId;	6✔
100	}
101
102	public static boolean isUnloadedStatus(String status) {
103	if (status.equals("seen")) return true; // only exists in "accounts_loading"?	×
104	if (status.equals("skipped")) return true;	×
105	return false;	×
106	}
107
108	public static boolean isCoreLoadedStatus(String status) {
109	if (status.equals("visited")) return true; // only exists in "accounts_loading"?	×
110	if (status.equals("expanded")) return true; // only exists in "accounts_loading"?	×
111	if (status.equals("processed")) return true; // only exists in "accounts_loading"?	×
112	if (status.equals("aggregated")) return true; // only exists in "accounts_loading"?	×
113	if (status.equals("approved")) return true; // only exists in "accounts_loading"?	×
114	if (status.equals("contested")) return true;	×
115	if (status.equals("toLoad")) return true; // only exists in "accounts_loading"?	×
116	if (status.equals("loaded")) return true;	×
117	return false;	×
118	}
119
120	public static boolean isFullyLoadedStatus(String status) {
121	if (status.equals("loaded")) return true;	×
122	return false;	×
123	}
124
125	private static ValueFactory vf = SimpleValueFactory.getInstance();	6✔
126	public static final IRI APPROVES_OF = vf.createIRI("http://purl.org/nanopub/x/approvesOf");	12✔
127
128	public static final String TYPE_JSON = "application/json";
129	public static final String TYPE_TRIG = "application/trig";
130	public static final String TYPE_JELLY = "application/x-jelly-rdf";
131	public static final String TYPE_JSONLD = "application/ld+json";
132	public static final String TYPE_NQUADS = "application/n-quads";
133	public static final String TYPE_TRIX = "application/trix";
134	public static final String TYPE_HTML = "text/html";
135
136	// Content types supported on a ListPage
137	public static final String SUPPORTED_TYPES_LIST = TYPE_JSON + "," + TYPE_JELLY + "," + TYPE_HTML;
138	// Content types supported on a NanopubPage
139	public static final String SUPPORTED_TYPES_NANOPUB = TYPE_TRIG + "," + TYPE_JELLY + "," + TYPE_JSONLD + "," + TYPE_NQUADS + "," + TYPE_TRIX + "," + TYPE_HTML;
140
141	private static Map<String, String> extensionTypeMap;
142
143	public static String getType(String extension) {
144	if (extension == null) {	×
145	return null;	×
146	}
147	if (extensionTypeMap == null) {	×
148	extensionTypeMap = new HashMap<>();	×
149	extensionTypeMap.put("trig", TYPE_TRIG);	×
150	extensionTypeMap.put("jelly", TYPE_JELLY);	×
151	extensionTypeMap.put("jsonld", TYPE_JSONLD);	×
152	extensionTypeMap.put("nq", TYPE_NQUADS);	×
153	extensionTypeMap.put("xml", TYPE_TRIX);	×
154	extensionTypeMap.put("html", TYPE_HTML);	×
155	extensionTypeMap.put("json", TYPE_JSON);	×
156	}
157	return extensionTypeMap.get(extension);	×
158	}
159
160	private static List<String> peerUrls;
161
162	public static List<String> getPeerUrls() {
163	if (peerUrls == null) {	×
164	String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");	×
165	String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");	×
166	if (!envPeerUrls.isEmpty()) {	×
167	peerUrls = new ArrayList<>();	×
168	for (String peerUrl : envPeerUrls.split(";")) {	×
169	if (thisRegistryUrl.equals(peerUrl)) continue;	×
170	peerUrls.add(peerUrl);	×
171	}
172	} else {
173	NanopubSetting setting;
174	try {
175	setting = getSetting();	×
176	} catch (Exception ex) {	×
177	throw new RuntimeException(ex);	×
178	}	×
179	peerUrls = new ArrayList<>();	×
180	for (IRI iri : setting.getBootstrapServices()) {	×
181	String peerUrl = iri.stringValue();	×
182	if (thisRegistryUrl.equals(peerUrl)) continue;	×
183	peerUrls.add(peerUrl);	×
184	}	×
185	}
186	}
187	return peerUrls;	×
188	}
189
190	private static final String SETTING_FILE_PATH = Utils.getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");	12✔
191	private static NanopubSetting settingNp;
192
193	public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
194	if (settingNp == null) {	×
195	settingNp = new NanopubSetting(new NanopubImpl(new File(SETTING_FILE_PATH)));	×
196	}
197	return settingNp;	×
198	}
199
200	public static String getRandomPeer() throws RDF4JException {
201	List<String> peerUrls = getPeerUrls();	×
202	return peerUrls.get(random.nextInt(peerUrls.size()));	×
203	}
204
205	private static Random random = new Random();	12✔
206
207	public static Random getRandom() {
208	return random;	×
209	}
210
211	private static Gson g = new Gson();	12✔
212	private static Type listType = new TypeToken<List<String>>() {	21✔
213	}.getType();	6✔
214
215	public static List<String> retrieveListFromJsonUrl(String url) throws JsonIOException, JsonSyntaxException, IOException, URISyntaxException {
216	return g.fromJson(new InputStreamReader(new URI(url).toURL().openStream()), listType);	×
217	}
218
219	}

knowledgepixels / nanopub-registry / 20413250445

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous