17767759901

Committed 16 Sep 2025 01:40PM UTC coverage: 71.59% (-0.2%) from 71.741%

Build Type

push

github

Committed by Ziroli Plutschow

Commit Message

Replacing newest System.err with slf4j logging

- Note: Also upgraded mockito, since it's transient dependency byte-buddy could not handle a jvm > 21

Run Details

233 of 350 branches covered (66.57%)

Branch coverage included in aggregate %.

591 of 801 relevant lines covered (73.78%)

3.72 hits per line

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86.67

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

package com.knowledgepixels.query;

import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.MultiNanopubRdfHandler;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

/**
 * Local loader left here in case it's needed for testing or when the Jelly loader breaks.
 */
public class LocalNanopubLoader {

    private static final Logger log = LoggerFactory.getLogger(LocalNanopubLoader.class);

    private LocalNanopubLoader() {
    }  // no instances allowed

    /**
     * File containing URIs of nanopubs to load.
     */
    public final static File loadUrisFile = new File("load/nanopub-uris.txt");

    /**
     * File containing nanopubs in TRIG format to load.
     */
    public final static File loadNanopubsFile = new File("load/nanopubs.trig.gz");

    private static final int WAIT_SECONDS = Utils.getEnvInt("INIT_WAIT_SECONDS", 120);

    /**
     * Load nanopubs from local files.
     *
     * @return true if local nanopubs were found and loaded, false otherwise
     */
    public static boolean init() {
        // FIXME should this be loadNanopubsFile.exists() || loadUrisFile.exists()?
        if (!(loadNanopubsFile.exists() || loadNanopubsFile.exists())) {
            log.info("No local nanopub files for loading found. Moving on to loading via Jelly...");
            return false;
        }
        log.info("Waiting {} seconds to make sure the triple store is up...", WAIT_SECONDS);
        try {
            for (int w = 0; w < WAIT_SECONDS; w++) {
                log.info("Waited {} seconds...", w);
                Thread.sleep(1000);
            }
        } catch (InterruptedException ex) {
            // ignore
        }

        log.info("Loading the local list of nanopubs...");
        load();
        return true;
    }

    static void load() {
        if (!loadUrisFile.exists()) {
            log.info("No local nanopub URI file found.");
        } else {
            try (BufferedReader reader = new BufferedReader(new FileReader(loadUrisFile))) {
                String line = reader.readLine();
                while (line != null) {
                    NanopubLoader.load(line);
                    line = reader.readLine();
                }
            } catch (IOException ex) {
                log.info("Loading nanopubs failed.", ex);
            }
        }
        if (!loadNanopubsFile.exists()) {
            log.info("No local nanopub file found.");
        } else {
            try {
                MultiNanopubRdfHandler.process(RDFFormat.TRIG, loadNanopubsFile, np -> NanopubLoader.load(np, -1));
            } catch (IOException | MalformedNanopubException ex) {
                log.info("Loading nanopubs failed.", ex);
            }
        }
    }

}

1	package com.knowledgepixels.query;
2
3	import org.eclipse.rdf4j.rio.RDFFormat;
4	import org.nanopub.MalformedNanopubException;
5	import org.nanopub.MultiNanopubRdfHandler;
6	import org.slf4j.Logger;
7	import org.slf4j.LoggerFactory;
8
9	import java.io.BufferedReader;
10	import java.io.File;
11	import java.io.FileReader;
12	import java.io.IOException;
13
14	/**
15	* Local loader left here in case it's needed for testing or when the Jelly loader breaks.
16	*/
17	public class LocalNanopubLoader {
18
19	private static final Logger log = LoggerFactory.getLogger(LocalNanopubLoader.class);	3✔
20
21	private LocalNanopubLoader() {
22	} // no instances allowed
23
24	/**
25	* File containing URIs of nanopubs to load.
26	*/
27	public final static File loadUrisFile = new File("load/nanopub-uris.txt");	5✔
28
29	/**
30	* File containing nanopubs in TRIG format to load.
31	*/
32	public final static File loadNanopubsFile = new File("load/nanopubs.trig.gz");	5✔
33
34	private static final int WAIT_SECONDS = Utils.getEnvInt("INIT_WAIT_SECONDS", 120);	5✔
35
36	/**
37	* Load nanopubs from local files.
38	*
39	* @return true if local nanopubs were found and loaded, false otherwise
40	*/
41	public static boolean init() {
42	// FIXME should this be loadNanopubsFile.exists() \|\| loadUrisFile.exists()?
43	if (!(loadNanopubsFile.exists() \|\| loadNanopubsFile.exists())) {	6!
44	log.info("No local nanopub files for loading found. Moving on to loading via Jelly...");	3✔
45	return false;	2✔
46	}
47	log.info("Waiting {} seconds to make sure the triple store is up...", WAIT_SECONDS);	5✔
48	try {
49	for (int w = 0; w < WAIT_SECONDS; w++) {	7✔
50	log.info("Waited {} seconds...", w);	5✔
51	Thread.sleep(1000);	2✔
52	}
53	} catch (InterruptedException ex) {	×
54	// ignore
55	}	1✔
56
57	log.info("Loading the local list of nanopubs...");	3✔
58	load();	1✔
59	return true;	2✔
60	}
61
62	static void load() {
63	if (!loadUrisFile.exists()) {	3✔
64	log.info("No local nanopub URI file found.");	4✔
65	} else {
66	try (BufferedReader reader = new BufferedReader(new FileReader(loadUrisFile))) {	8✔
67	String line = reader.readLine();	3✔
68	while (line != null) {	2✔
69	NanopubLoader.load(line);	2✔
70	line = reader.readLine();	4✔
71	}
72	} catch (IOException ex) {	×
73	log.info("Loading nanopubs failed.", ex);	×
74	}	1✔
75	}
76	if (!loadNanopubsFile.exists()) {	3✔
77	log.info("No local nanopub file found.");	4✔
78	} else {
79	try {
80	MultiNanopubRdfHandler.process(RDFFormat.TRIG, loadNanopubsFile, np -> NanopubLoader.load(np, -1));	×
81	} catch (IOException \| MalformedNanopubException ex) {	1✔
82	log.info("Loading nanopubs failed.", ex);	4✔
83	}	×
84	}
85	}	1✔
86
87	}

knowledgepixels / nanopub-query / 17767759901

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