24727603152

Committed 21 Apr 2026 02:18PM UTC coverage: 31.808% (+0.3%) from 31.558%

Build # 24727603152

Build Type

push

github

Committed by

ashleycaselli

Commit Message

chore(logging): enhance info error handling in Nanopub processing

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280 of 986 branches covered (28.4%)

Branch coverage included in aggregate %.

839 of 2532 relevant lines covered (33.14%)

5.5 hits per line

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92.75

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.util.Values;
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.InputStream;
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.*;

/**
 * Utility class for the Nanopub Registry.
 */
public class Utils {

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

    private Utils() {
    }  // no instances allowed

    private static volatile String version;

    /**
     * Returns the registry's version (from Maven at build time, via a filtered
     * {@code version.properties} resource). Returns {@code "unknown"} if the
     * resource is unavailable.
     */
    public static String getVersion() {
        String v = version;
        if (v != null) {
            return v;
        }
        Properties p = new Properties();
        try (InputStream in = Utils.class.getResourceAsStream("/version.properties")) {
            if (in != null) {
                p.load(in);
            }
        } catch (IOException ex) {
            logger.warn("Could not read version.properties", ex);
        }
        v = p.getProperty("version", "unknown");
        version = v;
        return v;
    }

    public static String getMimeType(RoutingContext context, String supported) {
        List<String> supportedList = Arrays.asList(StringUtils.split(supported, ','));
        String mimeType = supportedList.getFirst();
        String acceptHeader = context.request().getHeader("Accept");
        if (acceptHeader == null) {
            return mimeType;
        }
        try {
            mimeType = MIMEParse.bestMatch(supportedList, acceptHeader);
        } catch (Exception ex) {
            logger.error("Failed to parse Accept header '{}': {}", acceptHeader, ex.getMessage(), 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();
    }

    /**
     * Get the IDs of nanopublications invalidated by the given nanopublication.
     *
     * @param np the nanopublication to check
     * @return a set of IRI IDs of invalidated nanopublications
     */
    public static Set<IRI> getInvalidatedNanopubIds(Nanopub np) {
        Set<IRI> invalidatedNanopubs = new HashSet<>();
        for (Statement st : NanopubUtils.getStatements(np)) {
            if (!(st.getObject() instanceof IRI)) {
                continue;
            }
            Resource subject = st.getSubject();
            IRI predicate = st.getPredicate();
            if ((predicate.equals(NPX.RETRACTS) || predicate.equals(NPX.INVALIDATES)) || (predicate.equals(NPX.SUPERSEDES) && subject.equals(np.getUri()))) {
                if (TrustyUriUtils.isPotentialTrustyUri(st.getObject().stringValue())) {
                    invalidatedNanopubs.add((IRI) st.getObject());
                }
            }
        }
        return invalidatedNanopubs;
    }

    private static ReadsEnvironment ENV_READER = new ReadsEnvironment(System::getenv);

    /**
     * Set the environment reader (used for testing purposes).
     *
     * @param reader the environment reader to set
     */
    public static void setEnvReader(ReadsEnvironment reader) {
        ENV_READER = reader;
    }

    /**
     * Get an environment variable, returning a default value if not set.
     *
     * @param name         the name of the environment variable
     * @param defaultValue the default value to return if the variable is not set
     * @return the value of the environment variable, or the default value if not set
     */
    public static String getEnv(String name, String defaultValue) {
        logger.debug("Reading environment variable '{}'", name);
        String value = ENV_READER.getEnv(name);
        if (value == null) {
            value = defaultValue;
            logger.debug("Environment variable '{}' not set; using default: '{}'", name, defaultValue);
        }
        return value;
    }

    /**
     * Get the type hash for a given type, recording it in the database if necessary.
     *
     * @param mongoSession the MongoDB client session
     * @param type         the type to get the hash for
     * @return the type hash
     */
    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;
    }

    /**
     * Get a label for an agent ID, truncating if necessary.
     *
     * @param agentId the agent ID
     * @return the agent label
     */
    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;
    }

    /**
     * Check if the given status indicates an unloaded entry.
     *
     * @param status the status to check
     * @return true if the status indicates an unloaded entry, false otherwise
     */
    public static boolean isUnloadedStatus(String status) {
        if (status.equals(EntryStatus.seen.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        return status.equals(EntryStatus.skipped.getValue());
    }

    /**
     * Check if the given status indicates a core loaded entry.
     *
     * @param status the status to check
     * @return true if the status indicates a core loaded entry, false otherwise
     */
    public static boolean isCoreLoadedStatus(String status) {
        if (status.equals(EntryStatus.visited.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        if (status.equals(EntryStatus.expanded.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        if (status.equals(EntryStatus.processed.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        if (status.equals(EntryStatus.aggregated.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        if (status.equals(EntryStatus.approved.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        if (status.equals(EntryStatus.contested.getValue())) {
            return true;
        }
        if (status.equals(EntryStatus.toLoad.getValue())) {
            return true;  // only exists in "accounts_loading"?
        }
        return status.equals(EntryStatus.loaded.getValue());
    }

    /**
     * Check if the given status indicates a fully loaded entry.
     *
     * @param status the status to check
     * @return true if the status indicates a fully loaded entry, false otherwise
     */
    public static boolean isFullyLoadedStatus(String status) {
        return status.equals(EntryStatus.loaded.getValue());
    }

    public static final IRI APPROVES_OF = Values.iri("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;

    /**
     * Get the type corresponding to a given file extension.
     *
     * @param extension the file extension
     * @return the corresponding MIME type, or null if not found
     */
    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;

    /**
     * Get the list of peer registry URLs.
     *
     * @return the list of peer registry URLs
     */
    public static List<String> getPeerUrls() {
        if (peerUrls == null) {
            peerUrls = new ArrayList<>();
            String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");
            String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");
            if (!envPeerUrls.isEmpty()) {
                for (String peerUrl : envPeerUrls.trim().split("\\s+")) {
                    if (thisRegistryUrl.equals(peerUrl)) {
                        continue;
                    }
                    peerUrls.add(peerUrl);
                }
            } else {
                NanopubSetting setting;
                try {
                    setting = getSetting();
                } catch (MalformedNanopubException | IOException ex) {
                    logger.error("Failed to load registry setting from file", ex);
                    throw new RuntimeException(ex);
                }
                for (IRI iri : setting.getBootstrapServices()) {
                    String peerUrl = iri.stringValue();
                    if (thisRegistryUrl.equals(peerUrl)) {
                        continue;
                    }
                    peerUrls.add(peerUrl);
                }
            }
        }
        return peerUrls;
    }

    private static volatile NanopubSetting settingNp;

    /**
     * Get the nanopublication setting.
     *
     * @return the nanopublication setting
     * @throws RDF4JException            if there is an error retrieving the setting
     * @throws MalformedNanopubException if the setting nanopublication is malformed
     * @throws IOException               if there is an I/O error
     */
    public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
        if (settingNp == null) {
            synchronized (Utils.class) {
                if (settingNp == null) {
                    String settingPath = getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");
                    settingNp = new NanopubSetting(new NanopubImpl(new File(settingPath)));
                }
            }
        }
        return settingNp;
    }

    /**
     * Get a random peer registry URL.
     *
     * @return a random peer registry URL
     * @throws RDF4JException if there is an error retrieving the peer URLs
     */
    public static String getRandomPeer() throws RDF4JException {
        List<String> peerUrls = getPeerUrls();
        return peerUrls.get(random.nextInt(peerUrls.size()));
    }

    private static final Random random = new Random();

    /**
     * Get the random number generator.
     *
     * @return the random number generator
     */
    public static Random getRandom() {
        return random;
    }

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

    /**
     * Retrieve a list of strings from a JSON URL.
     *
     * @param url the URL to retrieve the JSON from
     * @return the list of strings
     * @throws JsonIOException     if there is an error reading the JSON
     * @throws JsonSyntaxException if the JSON syntax is invalid
     * @throws IOException         if there is an I/O error
     * @throws URISyntaxException  if the URL syntax is invalid
     */
    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.util.Values;
19	import org.nanopub.MalformedNanopubException;
20	import org.nanopub.Nanopub;
21	import org.nanopub.NanopubImpl;
22	import org.nanopub.NanopubUtils;
23	import org.nanopub.extra.setting.NanopubSetting;
24	import org.nanopub.vocabulary.NPX;
25	import org.slf4j.Logger;
26	import org.slf4j.LoggerFactory;
27
28	import java.io.File;
29	import java.io.IOException;
30	import java.io.InputStream;
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	/**
40	* Utility class for the Nanopub Registry.
41	*/
42	public class Utils {
43
44	private static final Logger logger = LoggerFactory.getLogger(Utils.class);	9✔
45
46	private Utils() {
47	} // no instances allowed
48
49	private static volatile String version;
50
51	/**
52	* Returns the registry's version (from Maven at build time, via a filtered
53	* {@code version.properties} resource). Returns {@code "unknown"} if the
54	* resource is unavailable.
55	*/
56	public static String getVersion() {
57	String v = version;	6✔
58	if (v != null) {	6✔
59	return v;	6✔
60	}
61	Properties p = new Properties();	12✔
62	try (InputStream in = Utils.class.getResourceAsStream("/version.properties")) {	12✔
63	if (in != null) {	6!
64	p.load(in);	9✔
65	}
66	} catch (IOException ex) {	×
67	logger.warn("Could not read version.properties", ex);	×
68	}	3✔
69	v = p.getProperty("version", "unknown");	15✔
70	version = v;	6✔
71	return v;	6✔
72	}
73
74	public static String getMimeType(RoutingContext context, String supported) {
75	List<String> supportedList = Arrays.asList(StringUtils.split(supported, ','));	15✔
76	String mimeType = supportedList.getFirst();	12✔
77	String acceptHeader = context.request().getHeader("Accept");	15✔
78	if (acceptHeader == null) {	6✔
79	return mimeType;	6✔
80	}
81	try {
82	mimeType = MIMEParse.bestMatch(supportedList, acceptHeader);	12✔
83	} catch (Exception ex) {	×
84	logger.error("Failed to parse Accept header '{}': {}", acceptHeader, ex.getMessage(), ex);	×
85	}	3✔
86	return mimeType;	6✔
87	}
88
89	public static String urlEncode(Object o) {
90	return URLEncoder.encode((o == null ? "" : o.toString()), StandardCharsets.UTF_8);	27✔
91	}
92
93	public static String getHash(String s) {
94	return Hashing.sha256().hashString(s, Charsets.UTF_8).toString();	18✔
95	}
96
97	/**
98	* Get the IDs of nanopublications invalidated by the given nanopublication.
99	*
100	* @param np the nanopublication to check
101	* @return a set of IRI IDs of invalidated nanopublications
102	*/
103	public static Set<IRI> getInvalidatedNanopubIds(Nanopub np) {
104	Set<IRI> invalidatedNanopubs = new HashSet<>();	12✔
105	for (Statement st : NanopubUtils.getStatements(np)) {	33✔
106	if (!(st.getObject() instanceof IRI)) {	12✔
107	continue;	3✔
108	}
109	Resource subject = st.getSubject();	9✔
110	IRI predicate = st.getPredicate();	9✔
111	if ((predicate.equals(NPX.RETRACTS) \|\| predicate.equals(NPX.INVALIDATES)) \|\| (predicate.equals(NPX.SUPERSEDES) && subject.equals(np.getUri()))) {	51!
112	if (TrustyUriUtils.isPotentialTrustyUri(st.getObject().stringValue())) {	15!
113	invalidatedNanopubs.add((IRI) st.getObject());	18✔
114	}
115	}
116	}	3✔
117	return invalidatedNanopubs;	6✔
118	}
119
120	private static ReadsEnvironment ENV_READER = new ReadsEnvironment(System::getenv);	15✔
121
122	/**
123	* Set the environment reader (used for testing purposes).
124	*
125	* @param reader the environment reader to set
126	*/
127	public static void setEnvReader(ReadsEnvironment reader) {
128	ENV_READER = reader;	6✔
129	}	3✔
130
131	/**
132	* Get an environment variable, returning a default value if not set.
133	*
134	* @param name the name of the environment variable
135	* @param defaultValue the default value to return if the variable is not set
136	* @return the value of the environment variable, or the default value if not set
137	*/
138	public static String getEnv(String name, String defaultValue) {
139	logger.debug("Reading environment variable '{}'", name);	12✔
140	String value = ENV_READER.getEnv(name);	12✔
141	if (value == null) {	6✔
142	value = defaultValue;	6✔
143	logger.debug("Environment variable '{}' not set; using default: '{}'", name, defaultValue);	15✔
144	}
145	return value;	6✔
146	}
147
148	/**
149	* Get the type hash for a given type, recording it in the database if necessary.
150	*
151	* @param mongoSession the MongoDB client session
152	* @param type the type to get the hash for
153	* @return the type hash
154	*/
155	public static String getTypeHash(ClientSession mongoSession, Object type) {
156	String typeHash = Utils.getHash(type.toString());	12✔
157	if (type.toString().equals("$")) {	15✔
158	typeHash = "$";	9✔
159	} else {
160	RegistryDB.recordHash(mongoSession, type.toString());	12✔
161	}
162	return typeHash;	6✔
163	}
164
165	/**
166	* Get a label for an agent ID, truncating if necessary.
167	*
168	* @param agentId the agent ID
169	* @return the agent label
170	*/
171	public static String getAgentLabel(String agentId) {
172	if (agentId == null \|\| agentId.isBlank()) {	15✔
173	throw new IllegalArgumentException("Agent ID cannot be null or blank");	15✔
174	}
175	agentId = agentId.replaceFirst("^https://orcid\\.org/", "orcid:");	15✔
176	if (agentId.length() > 55) {	12✔
177	return agentId.substring(0, 50) + "...";	18✔
178	}
179	return agentId;	6✔
180	}
181
182	/**
183	* Check if the given status indicates an unloaded entry.
184	*
185	* @param status the status to check
186	* @return true if the status indicates an unloaded entry, false otherwise
187	*/
188	public static boolean isUnloadedStatus(String status) {
189	if (status.equals(EntryStatus.seen.getValue())) {	15✔
190	return true; // only exists in "accounts_loading"?	6✔
191	}
192	return status.equals(EntryStatus.skipped.getValue());	15✔
193	}
194
195	/**
196	* Check if the given status indicates a core loaded entry.
197	*
198	* @param status the status to check
199	* @return true if the status indicates a core loaded entry, false otherwise
200	*/
201	public static boolean isCoreLoadedStatus(String status) {
202	if (status.equals(EntryStatus.visited.getValue())) {	15✔
203	return true; // only exists in "accounts_loading"?	6✔
204	}
205	if (status.equals(EntryStatus.expanded.getValue())) {	15✔
206	return true; // only exists in "accounts_loading"?	6✔
207	}
208	if (status.equals(EntryStatus.processed.getValue())) {	15✔
209	return true; // only exists in "accounts_loading"?	6✔
210	}
211	if (status.equals(EntryStatus.aggregated.getValue())) {	15✔
212	return true; // only exists in "accounts_loading"?	6✔
213	}
214	if (status.equals(EntryStatus.approved.getValue())) {	15✔
215	return true; // only exists in "accounts_loading"?	6✔
216	}
217	if (status.equals(EntryStatus.contested.getValue())) {	15✔
218	return true;	6✔
219	}
220	if (status.equals(EntryStatus.toLoad.getValue())) {	15✔
221	return true; // only exists in "accounts_loading"?	6✔
222	}
223	return status.equals(EntryStatus.loaded.getValue());	15✔
224	}
225
226	/**
227	* Check if the given status indicates a fully loaded entry.
228	*
229	* @param status the status to check
230	* @return true if the status indicates a fully loaded entry, false otherwise
231	*/
232	public static boolean isFullyLoadedStatus(String status) {
233	return status.equals(EntryStatus.loaded.getValue());	15✔
234	}
235
236	public static final IRI APPROVES_OF = Values.iri("http://purl.org/nanopub/x/approvesOf");	9✔
237
238	public static final String TYPE_JSON = "application/json";
239	public static final String TYPE_TRIG = "application/trig";
240	public static final String TYPE_JELLY = "application/x-jelly-rdf";
241	public static final String TYPE_JSONLD = "application/ld+json";
242	public static final String TYPE_NQUADS = "application/n-quads";
243	public static final String TYPE_TRIX = "application/trix";
244	public static final String TYPE_HTML = "text/html";
245
246	// Content types supported on a ListPage
247	public static final String SUPPORTED_TYPES_LIST = TYPE_JSON + "," + TYPE_JELLY + "," + TYPE_HTML;
248	// Content types supported on a NanopubPage
249	public static final String SUPPORTED_TYPES_NANOPUB = TYPE_TRIG + "," + TYPE_JELLY + "," + TYPE_JSONLD + "," + TYPE_NQUADS + "," + TYPE_TRIX + "," + TYPE_HTML;
250
251	private static Map<String, String> extensionTypeMap;
252
253	/**
254	* Get the type corresponding to a given file extension.
255	*
256	* @param extension the file extension
257	* @return the corresponding MIME type, or null if not found
258	*/
259	public static String getType(String extension) {
260	if (extension == null) {	6✔
261	return null;	6✔
262	}
263	if (extensionTypeMap == null) {	6✔
264	extensionTypeMap = new HashMap<>();	12✔
265	extensionTypeMap.put("trig", TYPE_TRIG);	15✔
266	extensionTypeMap.put("jelly", TYPE_JELLY);	15✔
267	extensionTypeMap.put("jsonld", TYPE_JSONLD);	15✔
268	extensionTypeMap.put("nq", TYPE_NQUADS);	15✔
269	extensionTypeMap.put("xml", TYPE_TRIX);	15✔
270	extensionTypeMap.put("html", TYPE_HTML);	15✔
271	extensionTypeMap.put("json", TYPE_JSON);	15✔
272	}
273	return extensionTypeMap.get(extension);	15✔
274	}
275
276	private static List<String> peerUrls;
277
278	/**
279	* Get the list of peer registry URLs.
280	*
281	* @return the list of peer registry URLs
282	*/
283	public static List<String> getPeerUrls() {
284	if (peerUrls == null) {	6✔
285	peerUrls = new ArrayList<>();	12✔
286	String envPeerUrls = getEnv("REGISTRY_PEER_URLS", "");	12✔
287	String thisRegistryUrl = getEnv("REGISTRY_SERVICE_URL", "");	12✔
288	if (!envPeerUrls.isEmpty()) {	9✔
289	for (String peerUrl : envPeerUrls.trim().split("\\s+")) {	60✔
290	if (thisRegistryUrl.equals(peerUrl)) {	12!
291	continue;	×
292	}
293	peerUrls.add(peerUrl);	12✔
294	}
295	} else {
296	NanopubSetting setting;
297	try {
298	setting = getSetting();	6✔
299	} catch (MalformedNanopubException \| IOException ex) {	3✔
300	logger.error("Failed to load registry setting from file", ex);	12✔
301	throw new RuntimeException(ex);	15✔
302	}	3✔
303	for (IRI iri : setting.getBootstrapServices()) {	33✔
304	String peerUrl = iri.stringValue();	9✔
305	if (thisRegistryUrl.equals(peerUrl)) {	12!
306	continue;	×
307	}
308	peerUrls.add(peerUrl);	12✔
309	}	3✔
310	}
311	}
312	return peerUrls;	6✔
313	}
314
315	private static volatile NanopubSetting settingNp;
316
317	/**
318	* Get the nanopublication setting.
319	*
320	* @return the nanopublication setting
321	* @throws RDF4JException if there is an error retrieving the setting
322	* @throws MalformedNanopubException if the setting nanopublication is malformed
323	* @throws IOException if there is an I/O error
324	*/
325	public static NanopubSetting getSetting() throws RDF4JException, MalformedNanopubException, IOException {
326	if (settingNp == null) {	6✔
327	synchronized (Utils.class) {	12✔
328	if (settingNp == null) {	6!
329	String settingPath = getEnv("REGISTRY_SETTING_FILE", "/data/setting.trig");	12✔
330	settingNp = new NanopubSetting(new NanopubImpl(new File(settingPath)));	33✔
331	}
332	}	9✔
333	}
334	return settingNp;	6✔
335	}
336
337	/**
338	* Get a random peer registry URL.
339	*
340	* @return a random peer registry URL
341	* @throws RDF4JException if there is an error retrieving the peer URLs
342	*/
343	public static String getRandomPeer() throws RDF4JException {
344	List<String> peerUrls = getPeerUrls();	6✔
345	return peerUrls.get(random.nextInt(peerUrls.size()));	24✔
346	}
347
348	private static final Random random = new Random();	12✔
349
350	/**
351	* Get the random number generator.
352	*
353	* @return the random number generator
354	*/
355	public static Random getRandom() {
356	return random;	6✔
357	}
358
359	private static final Gson g = new Gson();	12✔
360	private static Type listType = new TypeToken<List<String>>() {	21✔
361	}.getType();	6✔
362
363	/**
364	* Retrieve a list of strings from a JSON URL.
365	*
366	* @param url the URL to retrieve the JSON from
367	* @return the list of strings
368	* @throws JsonIOException if there is an error reading the JSON
369	* @throws JsonSyntaxException if the JSON syntax is invalid
370	* @throws IOException if there is an I/O error
371	* @throws URISyntaxException if the URL syntax is invalid
372	*/
373	public static List<String> retrieveListFromJsonUrl(String url) throws JsonIOException, JsonSyntaxException, IOException, URISyntaxException {
374	return g.fromJson(new InputStreamReader(new URI(url).toURL().openStream()), listType);	×
375	}
376
377	}

knowledgepixels / nanopub-registry / 24727603152

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