20441087941

Committed 22 Dec 2025 06:51PM UTC coverage: 1.591% (+0.04%) from 1.554%

Build # 20441087941

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor(exceptions): replace RuntimeExceptions with custom exception classes

Run Details

6 of 592 branches covered (1.01%)

Branch coverage included in aggregate %.

32 of 1797 relevant lines covered (1.78%)

0.23 hits per line

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

14.47

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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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 static final Logger logger = LoggerFactory.getLogger(Utils.class);

    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 (MalformedNanopubException | IOException ex) {
                    logger.error("Error loading registry setting", 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	import org.slf4j.Logger;
27	import org.slf4j.LoggerFactory;
28
29	import java.io.File;
30	import java.io.IOException;
31	import java.io.InputStreamReader;
32	import java.lang.reflect.Type;
33	import java.net.URI;
34	import java.net.URISyntaxException;
35	import java.net.URLEncoder;
36	import java.nio.charset.StandardCharsets;
37	import java.util.*;
38
39	public class Utils {
40
41	private static final Logger logger = LoggerFactory.getLogger(Utils.class);	9✔
42
43	private Utils() {
44	} // no instances allowed
45
46	public static String getMimeType(RoutingContext context, String supported) {
47	List<String> supportedList = Arrays.asList(StringUtils.split(supported, ','));	×
48	String mimeType = supportedList.getFirst();	×
49	try {
50	mimeType = MIMEParse.bestMatch(supportedList, context.request().getHeader("Accept"));	×
51	} catch (Exception ex) {	×
52	}	×
53	return mimeType;	×
54	}
55
56	public static String urlEncode(Object o) {
57	return URLEncoder.encode((o == null ? "" : o.toString()), StandardCharsets.UTF_8);	×
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 String TYPE_JSON = "application/json";
133	public static final String TYPE_TRIG = "application/trig";
134	public static final String TYPE_JELLY = "application/x-jelly-rdf";
135	public static final String TYPE_JSONLD = "application/ld+json";
136	public static final String TYPE_NQUADS = "application/n-quads";
137	public static final String TYPE_TRIX = "application/trix";
138	public static final String TYPE_HTML = "text/html";
139
140	// Content types supported on a ListPage
141	public static final String SUPPORTED_TYPES_LIST = TYPE_JSON + "," + TYPE_JELLY + "," + TYPE_HTML;
142	// Content types supported on a NanopubPage
143	public static final String SUPPORTED_TYPES_NANOPUB = TYPE_TRIG + "," + TYPE_JELLY + "," + TYPE_JSONLD + "," + TYPE_NQUADS + "," + TYPE_TRIX + "," + TYPE_HTML;
144
145	private static Map<String, String> extensionTypeMap;
146
147	public static String getType(String extension) {
148	if (extension == null) {	×
149	return null;	×
150	}
151	if (extensionTypeMap == null) {	×
152	extensionTypeMap = new HashMap<>();	×
153	extensionTypeMap.put("trig", TYPE_TRIG);	×
154	extensionTypeMap.put("jelly", TYPE_JELLY);	×
155	extensionTypeMap.put("jsonld", TYPE_JSONLD);	×
156	extensionTypeMap.put("nq", TYPE_NQUADS);	×
157	extensionTypeMap.put("xml", TYPE_TRIX);	×
158	extensionTypeMap.put("html", TYPE_HTML);	×
159	extensionTypeMap.put("json", TYPE_JSON);	×
160	}
161	return extensionTypeMap.get(extension);	×
162	}
163
164	private static List<String> peerUrls;
165
166	public static List<String> getPeerUrls() {
167	if (peerUrls == null) {	×
168	String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");	×
169	String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");	×
170	if (!envPeerUrls.isEmpty()) {	×
171	peerUrls = new ArrayList<>();	×
172	for (String peerUrl : envPeerUrls.split(";")) {	×
173	if (thisRegistryUrl.equals(peerUrl)) continue;	×
174	peerUrls.add(peerUrl);	×
175	}
176	} else {
177	NanopubSetting setting;
178	try {
179	setting = getSetting();	×
180	} catch (MalformedNanopubException \| IOException ex) {	×
181	logger.error("Error loading registry setting", ex);	×
182	throw new RuntimeException(ex);	×
183	}	×
184	peerUrls = new ArrayList<>();	×
185	for (IRI iri : setting.getBootstrapServices()) {	×
186	String peerUrl = iri.stringValue();	×
187	if (thisRegistryUrl.equals(peerUrl)) continue;	×
188	peerUrls.add(peerUrl);	×
189	}	×
190	}
191	}
192	return peerUrls;	×
193	}
194
195	private static final String SETTING_FILE_PATH = Utils.getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");	12✔
196	private static NanopubSetting settingNp;
197
198	public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
199	if (settingNp == null) {	×
200	settingNp = new NanopubSetting(new NanopubImpl(new File(SETTING_FILE_PATH)));	×
201	}
202	return settingNp;	×
203	}
204
205	public static String getRandomPeer() throws RDF4JException {
206	List<String> peerUrls = getPeerUrls();	×
207	return peerUrls.get(random.nextInt(peerUrls.size()));	×
208	}
209
210	private static Random random = new Random();	12✔
211
212	public static Random getRandom() {
213	return random;	×
214	}
215
216	private static Gson g = new Gson();	12✔
217	private static Type listType = new TypeToken<List<String>>() {	21✔
218	}.getType();	6✔
219
220	public static List<String> retrieveListFromJsonUrl(String url) throws JsonIOException, JsonSyntaxException, IOException, URISyntaxException {
221	return g.fromJson(new InputStreamReader(new URI(url).toURL().openStream()), listType);	×
222	}
223
224	}

knowledgepixels / nanopub-registry / 20441087941

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