20413250445

Committed 21 Dec 2025 05:19PM UTC coverage: 0.924% (-0.03%) from 0.954%

Build # 20413250445

Build Type

push

github

Committed by

ashleycaselli

Commit Message

chore: minor code cleanup

Run Details

6 of 592 branches covered (1.01%)

Branch coverage included in aggregate %.

16 of 1789 relevant lines covered (0.89%)

0.11 hits per line

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0.0

src/main/java/com/knowledgepixels/registry/NanopubPage.java

package com.knowledgepixels.registry;

import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
import com.mongodb.client.ClientSession;
import eu.neverblink.jelly.core.utils.IoUtils;
import io.vertx.ext.web.RoutingContext;
import org.apache.commons.lang.StringEscapeUtils;
import org.bson.Document;
import org.bson.types.Binary;
import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.NanopubUtils;

import java.io.IOException;

import static com.knowledgepixels.registry.RegistryDB.collection;
import static com.knowledgepixels.registry.RegistryDB.isSet;
import static com.knowledgepixels.registry.Utils.*;

public class NanopubPage extends Page {

    public static void show(RoutingContext context) {
        NanopubPage page;
        try (ClientSession s = RegistryDB.getClient().startSession()) {
            s.startTransaction();
            page = new NanopubPage(s, context);
            page.show();
        } catch (IOException ex) {
            ex.printStackTrace();
        } finally {
            context.response().end();
            // TODO Clean-up here?
        }
    }

    private NanopubPage(ClientSession mongoSession, RoutingContext context) {
        super(mongoSession, context);
    }

    protected void show() throws IOException {
        RoutingContext c = getContext();
        String ext = getExtension();
        String format = Utils.getType(ext);
        final String req = getRequestString();
        if (format == null) {
            format = Utils.getMimeType(c, SUPPORTED_TYPES_NANOPUB);
        }
        if (format == null) {
            c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());
            return;
        }

        var presentationFormat = getPresentationFormat();
        if (presentationFormat != null) {
            setRespContentType(presentationFormat);
        } else {
            setRespContentType(format);
        }

        if (req.matches("/np/RA[a-zA-Z0-9-_]{43}(\\.[a-z]+)?")) {
            String ac = req.replaceFirst("/np/(RA[a-zA-Z0-9-_]{43})(\\.[a-z]+)?", "$1");
            Document npDoc = collection("nanopubs").find(new Document("_id", ac)).first();
            if (npDoc == null) {
                if (!isSet(mongoSession, "serverInfo", "testInstance")) {
                    //getResp().sendError(404, "Not found: " + ac);
                    c.response().setStatusCode(307);
                    c.response().putHeader("Location", "https://np.knowledgepixels.com/" + ac);
                    return;
                } else {
                    c.response().setStatusCode(404).setStatusMessage("Not found: " + getFullRequest());
                    return;
                }
            }
            //                String url = ServerConf.getInfo().getPublicUrl();
            if (TYPE_TRIG.equals(format)) {
                println(npDoc.getString("content"));
            } else if (TYPE_JELLY.equals(format)) {
                if (presentationFormat != null && presentationFormat.startsWith("text")) {
                    // Parse the Jelly frame and return it as Protobuf Text Format Language
                    // https://protobuf.dev/reference/protobuf/textformat-spec/
                    // It's better than bombarding the browser with a binary file.
                    var frame = eu.neverblink.jelly.core.proto.google.v1.RdfStreamFrame
                            .parseFrom(((Binary) npDoc.get("jelly")).getData());
                    println(frame.toString());
                } else {
                    // To return this correctly, we would need to prepend the delimiter byte before the Jelly frame
                    // (the DB stores is non-delimited and the HTTP response must be delimited).
                    BufferOutputStream outputStream = new BufferOutputStream();
                    IoUtils.writeFrameAsDelimited(
                            ((Binary) npDoc.get("jelly")).getData(),
                            outputStream
                    );
                    c.response().write(outputStream.getBuffer());
                }
            } else if (format != null && format.equals(TYPE_NQUADS)) {
                outputNanopub(npDoc, RDFFormat.NQUADS);
            } else if (format != null && format.equals(TYPE_JSONLD)) {
                outputNanopub(npDoc, RDFFormat.JSONLD);
            } else if (format != null && format.equals(TYPE_TRIX)) {
                outputNanopub(npDoc, RDFFormat.TRIX);
            } else {
                printHtmlHeader("Nanopublication " + ac + " - Nanopub Registry");
                println("<h1>Nanopublication</h1>");
                println("<p><a href=\"/\">&lt; Home</a></p>");
                println("<h3>ID</h3>");
                String fullId = npDoc.getString("fullId");
                println("<p><a href=\"" + fullId + "\"><code>" + fullId + "</code></a></p>");
                println("<h3>Formats</h3>");
                println("<p>");
                println("<a href=\"/np/" + ac + ".trig\">.trig</a> |");
                println("<a href=\"/np/" + ac + ".trig.txt\">.trig.txt</a> |");
                println("<a href=\"/np/" + ac + ".jelly\">.jelly</a> |");
                println("<a href=\"/np/" + ac + ".jelly.txt\">.jelly.txt</a> |");
                println("<a href=\"/np/" + ac + ".jsonld\">.jsonld</a> |");
                println("<a href=\"/np/" + ac + ".jsonld.txt\">.jsonld.txt</a> |");
                println("<a href=\"/np/" + ac + ".nq\">.nq</a> |");
                println("<a href=\"/np/" + ac + ".nq.txt\">.nq.txt</a> |");
                println("<a href=\"/np/" + ac + ".xml\">.xml</a> |");
                println("<a href=\"/np/" + ac + ".xml.txt\">.xml.txt</a>");
                println("</p>");
                println("<h3>Content</h3>");
                println("<pre>");
                println(StringEscapeUtils.escapeHtml(npDoc.getString("content")));
                println("</pre>");
                printHtmlFooter();
            }
        } else {
            c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());
        }
    }

    private void outputNanopub(Document npDoc, RDFFormat rdfFormat) {
        RoutingContext c = getContext();
        try {
            Nanopub np = new NanopubImpl(npDoc.getString("content"), RDFFormat.TRIG);
            c.response().write(NanopubUtils.writeToString(np, rdfFormat), Charsets.UTF_8.toString());
        } catch (RDF4JException | MalformedNanopubException | IOException ex) {
            c.response().setStatusCode(500).setStatusMessage("Failed transforming nanopub: " + getFullRequest());
            ex.printStackTrace();
        }
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
4	import com.mongodb.client.ClientSession;
5	import eu.neverblink.jelly.core.utils.IoUtils;
6	import io.vertx.ext.web.RoutingContext;
7	import org.apache.commons.lang.StringEscapeUtils;
8	import org.bson.Document;
9	import org.bson.types.Binary;
10	import org.eclipse.rdf4j.common.exception.RDF4JException;
11	import org.eclipse.rdf4j.rio.RDFFormat;
12	import org.nanopub.MalformedNanopubException;
13	import org.nanopub.Nanopub;
14	import org.nanopub.NanopubImpl;
15	import org.nanopub.NanopubUtils;
16
17	import java.io.IOException;
18
19	import static com.knowledgepixels.registry.RegistryDB.collection;
20	import static com.knowledgepixels.registry.RegistryDB.isSet;
21	import static com.knowledgepixels.registry.Utils.*;
22
23	public class NanopubPage extends Page {
24
25	public static void show(RoutingContext context) {
26	NanopubPage page;
27	try (ClientSession s = RegistryDB.getClient().startSession()) {	×
28	s.startTransaction();	×
29	page = new NanopubPage(s, context);	×
30	page.show();	×
31	} catch (IOException ex) {	×
32	ex.printStackTrace();	×
33	} finally {
34	context.response().end();	×
35	// TODO Clean-up here?
36	}
37	}	×
38
39	private NanopubPage(ClientSession mongoSession, RoutingContext context) {
40	super(mongoSession, context);	×
41	}	×
42
43	protected void show() throws IOException {
44	RoutingContext c = getContext();	×
45	String ext = getExtension();	×
46	String format = Utils.getType(ext);	×
47	final String req = getRequestString();	×
48	if (format == null) {	×
49	format = Utils.getMimeType(c, SUPPORTED_TYPES_NANOPUB);	×
50	}
51	if (format == null) {	×
52	c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());	×
53	return;	×
54	}
55
56	var presentationFormat = getPresentationFormat();	×
57	if (presentationFormat != null) {	×
58	setRespContentType(presentationFormat);	×
59	} else {
60	setRespContentType(format);	×
61	}
62
63	if (req.matches("/np/RA[a-zA-Z0-9-_]{43}(\\.[a-z]+)?")) {	×
64	String ac = req.replaceFirst("/np/(RA[a-zA-Z0-9-_]{43})(\\.[a-z]+)?", "$1");	×
65	Document npDoc = collection("nanopubs").find(new Document("_id", ac)).first();	×
66	if (npDoc == null) {	×
67	if (!isSet(mongoSession, "serverInfo", "testInstance")) {	×
68	//getResp().sendError(404, "Not found: " + ac);
69	c.response().setStatusCode(307);	×
70	c.response().putHeader("Location", "https://np.knowledgepixels.com/" + ac);	×
71	return;	×
72	} else {
73	c.response().setStatusCode(404).setStatusMessage("Not found: " + getFullRequest());	×
74	return;	×
75	}
76	}
77	// String url = ServerConf.getInfo().getPublicUrl();
78	if (TYPE_TRIG.equals(format)) {	×
79	println(npDoc.getString("content"));	×
80	} else if (TYPE_JELLY.equals(format)) {	×
81	if (presentationFormat != null && presentationFormat.startsWith("text")) {	×
82	// Parse the Jelly frame and return it as Protobuf Text Format Language
83	// https://protobuf.dev/reference/protobuf/textformat-spec/
84	// It's better than bombarding the browser with a binary file.
85	var frame = eu.neverblink.jelly.core.proto.google.v1.RdfStreamFrame	×
86	.parseFrom(((Binary) npDoc.get("jelly")).getData());	×
87	println(frame.toString());	×
88	} else {	×
89	// To return this correctly, we would need to prepend the delimiter byte before the Jelly frame
90	// (the DB stores is non-delimited and the HTTP response must be delimited).
91	BufferOutputStream outputStream = new BufferOutputStream();	×
92	IoUtils.writeFrameAsDelimited(	×
93	((Binary) npDoc.get("jelly")).getData(),	×
94	outputStream
95	);
96	c.response().write(outputStream.getBuffer());	×
97	}	×
98	} else if (format != null && format.equals(TYPE_NQUADS)) {	×
99	outputNanopub(npDoc, RDFFormat.NQUADS);	×
100	} else if (format != null && format.equals(TYPE_JSONLD)) {	×
101	outputNanopub(npDoc, RDFFormat.JSONLD);	×
102	} else if (format != null && format.equals(TYPE_TRIX)) {	×
103	outputNanopub(npDoc, RDFFormat.TRIX);	×
104	} else {
105	printHtmlHeader("Nanopublication " + ac + " - Nanopub Registry");	×
106	println("<h1>Nanopublication</h1>");	×
107	println("<p><a href=\"/\">< Home</a></p>");	×
108	println("<h3>ID</h3>");	×
109	String fullId = npDoc.getString("fullId");	×
110	println("<p><a href=\"" + fullId + "\"><code>" + fullId + "</code></a></p>");	×
111	println("<h3>Formats</h3>");	×
112	println("<p>");	×
113	println("<a href=\"/np/" + ac + ".trig\">.trig</a> \|");	×
114	println("<a href=\"/np/" + ac + ".trig.txt\">.trig.txt</a> \|");	×
115	println("<a href=\"/np/" + ac + ".jelly\">.jelly</a> \|");	×
116	println("<a href=\"/np/" + ac + ".jelly.txt\">.jelly.txt</a> \|");	×
117	println("<a href=\"/np/" + ac + ".jsonld\">.jsonld</a> \|");	×
118	println("<a href=\"/np/" + ac + ".jsonld.txt\">.jsonld.txt</a> \|");	×
119	println("<a href=\"/np/" + ac + ".nq\">.nq</a> \|");	×
120	println("<a href=\"/np/" + ac + ".nq.txt\">.nq.txt</a> \|");	×
121	println("<a href=\"/np/" + ac + ".xml\">.xml</a> \|");	×
122	println("<a href=\"/np/" + ac + ".xml.txt\">.xml.txt</a>");	×
123	println("</p>");	×
124	println("<h3>Content</h3>");	×
125	println("<pre>");	×
126	println(StringEscapeUtils.escapeHtml(npDoc.getString("content")));	×
127	println("</pre>");	×
128	printHtmlFooter();	×
129	}
130	} else {	×
131	c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());	×
132	}
133	}	×
134
135	private void outputNanopub(Document npDoc, RDFFormat rdfFormat) {
136	RoutingContext c = getContext();	×
137	try {
138	Nanopub np = new NanopubImpl(npDoc.getString("content"), RDFFormat.TRIG);	×
139	c.response().write(NanopubUtils.writeToString(np, rdfFormat), Charsets.UTF_8.toString());	×
140	} catch (RDF4JException \| MalformedNanopubException \| IOException ex) {	×
141	c.response().setStatusCode(500).setStatusMessage("Failed transforming nanopub: " + getFullRequest());	×
142	ex.printStackTrace();	×
143	}	×
144	}	×
145
146	}

knowledgepixels / nanopub-registry / 20413250445

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