17769786051

Committed 16 Sep 2025 02:48PM UTC coverage: 71.59%. Remained the same

Build Type

push

github

Committed by Ziroli Plutschow

Commit Message

Stop tests from waiting 120s

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

Source File
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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 DEFAULT_WAIT_SECONDS = 120;

    /**
     * Load nanopubs from local files.
     *
     * @return true if local nanopubs were found and loaded, false otherwise
     */
    public static boolean init() {
        if (!(loadNanopubsFile.exists() || loadUrisFile.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...", getWaitSeconds());
        try {
            for (int w = 0; w < getWaitSeconds(); 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);
            }
        }
    }

    static int getWaitSeconds() {
        return Utils.getEnvInt("INIT_WAIT_SECONDS", DEFAULT_WAIT_SECONDS);
    }

}

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");	6✔
33
34	private static final int DEFAULT_WAIT_SECONDS = 120;
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	if (!(loadNanopubsFile.exists() \|\| loadUrisFile.exists())) {	6!
43	log.info("No local nanopub files for loading found. Moving on to loading via Jelly...");	3✔
44	return false;	2✔
45	}
46	log.info("Waiting {} seconds to make sure the triple store is up...", getWaitSeconds());	5✔
47	try {
48	for (int w = 0; w < getWaitSeconds(); w++) {	7✔
49	log.info("Waited {} seconds...", w);	5✔
50	Thread.sleep(1000);	2✔
51	}
52	} catch (InterruptedException ex) {	×
53	// ignore
54	}	1✔
55
56	log.info("Loading the local list of nanopubs...");	3✔
57	load();	1✔
58	return true;	2✔
59	}
60
61	static void load() {
62	if (!loadUrisFile.exists()) {	3✔
63	log.info("No local nanopub URI file found.");	4✔
64	} else {
65	try (BufferedReader reader = new BufferedReader(new FileReader(loadUrisFile))) {	8✔
66	String line = reader.readLine();	3✔
67	while (line != null) {	2✔
68	NanopubLoader.load(line);	2✔
69	line = reader.readLine();	4✔
70	}
71	} catch (IOException ex) {	×
72	log.info("Loading nanopubs failed.", ex);	×
73	}	1✔
74	}
75	if (!loadNanopubsFile.exists()) {	3✔
76	log.info("No local nanopub file found.");	4✔
77	} else {
78	try {
79	MultiNanopubRdfHandler.process(RDFFormat.TRIG, loadNanopubsFile, np -> NanopubLoader.load(np, -1));	×
80	} catch (IOException \| MalformedNanopubException ex) {	1✔
81	log.info("Loading nanopubs failed.", ex);	4✔
82	}	×
83	}
84	}	1✔
85
86	static int getWaitSeconds() {
87	return Utils.getEnvInt("INIT_WAIT_SECONDS", DEFAULT_WAIT_SECONDS);	4✔
88	}
89
90	}

knowledgepixels / nanopub-query / 17769786051

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