17039726108

Committed 18 Aug 2025 11:49AM UTC coverage: 30.826% (+2.9%) from 27.92%

Build # 17039726108

Build Type

push

github

Committed by

ashleycaselli

Commit Message

test(JellyNanopubLoader): add unit test for loadInitial method

Run Details

144 of 494 branches covered (29.15%)

Branch coverage included in aggregate %.

397 of 1261 relevant lines covered (31.48%)

1.46 hits per line

Source File
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84.44

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 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 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())) {
            System.err.println("No local nanopub files for loading found. Moving on to loading " +
                    "via Jelly...");
            return false;
        }
        System.err.println("Waiting " + WAIT_SECONDS + " seconds to make sure the triple store is up...");
        try {
            for (int w = 0; w < WAIT_SECONDS; w++) {
                System.err.println("Waited " + w + " seconds...");
                Thread.sleep(1000);
            }
        } catch (InterruptedException ex) {
            ex.printStackTrace();
        }

        System.err.println("Loading the local list of nanopubs...");
        load();
        return true;
    }

    static void load() {
        if (!loadUrisFile.exists()) {
            System.err.println("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) {
                ex.printStackTrace();
            }
        }
        if (!loadNanopubsFile.exists()) {
            System.err.println("No local nanopub file found.");
        } else {
            try {
                MultiNanopubRdfHandler.process(RDFFormat.TRIG, loadNanopubsFile, np -> NanopubLoader.load(np, -1));
            } catch (IOException | MalformedNanopubException ex) {
                ex.printStackTrace();
            }
        }
    }

}

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

knowledgepixels / nanopub-query / 17039726108

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