23243177209

Committed 18 Mar 2026 11:47AM UTC coverage: 30.21% (+4.3%) from 25.927%

Build # 23243177209

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #83 from knowledgepixels/feature/get-path-nanodash-forward

Add /get/ path that forwards to Nanodash for HTML requests

Coverage Stats

185 of 680 branches covered (27.21%)

Branch coverage included in aggregate %.

621 of 1988 relevant lines covered (31.24%)

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67.13

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 {

    static final String NANODASH_BASE_URL_DEFAULT = "https://nanodash.knowledgepixels.com/";

    static String getNanodashBaseUrl() {
        return Utils.getEnv("REGISTRY_NANODASH_BASE_URL", NANODASH_BASE_URL_DEFAULT);
    }

    private final boolean forwardHtml;

    public static void show(RoutingContext context) {
        show(context, false);
    }

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

    private NanopubPage(ClientSession mongoSession, RoutingContext context, boolean forwardHtml) {
        super(mongoSession, context);
        this.forwardHtml = forwardHtml;
    }

    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|get)/RA[a-zA-Z0-9-_]{43}(\\.[a-z]+)?")) {
            String ac = req.replaceFirst("/(np|get)/(RA[a-zA-Z0-9-_]{43})(\\.[a-z]+)?", "$2");
            Document npDoc = collection(Collection.NANOPUBS.toString()).find(new Document("_id", ac)).first();
            if (npDoc == null) {
                if (!isSet(mongoSession, Collection.SERVER_INFO.toString(), "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 if (forwardHtml && isHtmlRequested(c)) {
                String fullId = npDoc.getString("fullId");
                c.response().setStatusCode(302);
                c.response().putHeader("Location", getNanodashBaseUrl() + "explore?id=" + Utils.urlEncode(fullId));
                return;
            } else if (forwardHtml) {
                // Non-HTML default for /get/ path (e.g. Accept: */*): serve as trig
                setRespContentType(TYPE_TRIG);
                println(npDoc.getString("content"));
            } 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 static boolean isHtmlRequested(RoutingContext c) {
        String accept = c.request().getHeader("Accept");
        return accept != null && accept.contains("text/html");
    }

    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	static final String NANODASH_BASE_URL_DEFAULT = "https://nanodash.knowledgepixels.com/";
26
27	static String getNanodashBaseUrl() {
28	return Utils.getEnv("REGISTRY_NANODASH_BASE_URL", NANODASH_BASE_URL_DEFAULT);	12✔
29	}
30
31	private final boolean forwardHtml;
32
33	public static void show(RoutingContext context) {
34	show(context, false);	×
35	}	×
36
37	public static void show(RoutingContext context, boolean forwardHtml) {
38	NanopubPage page;
39	try (ClientSession s = RegistryDB.getClient().startSession()) {	9✔
40	s.startTransaction();	6✔
41	page = new NanopubPage(s, context, forwardHtml);	21✔
42	page.show();	6✔
43	} catch (IOException ex) {	×
44	ex.printStackTrace();	×
45	} finally {
46	context.response().end();	12✔
47	// TODO Clean-up here?
48	}
49	}	3✔
50
51	private NanopubPage(ClientSession mongoSession, RoutingContext context, boolean forwardHtml) {
52	super(mongoSession, context);	12✔
53	this.forwardHtml = forwardHtml;	9✔
54	}	3✔
55
56	protected void show() throws IOException {
57	RoutingContext c = getContext();	9✔
58	String ext = getExtension();	9✔
59	String format = Utils.getType(ext);	9✔
60	final String req = getRequestString();	9✔
61	if (format == null) {	6✔
62	format = Utils.getMimeType(c, SUPPORTED_TYPES_NANOPUB);	12✔
63	}
64	if (format == null) {	6!
65	c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());	×
66	return;	×
67	}
68
69	var presentationFormat = getPresentationFormat();	9✔
70	if (presentationFormat != null) {	6!
71	setRespContentType(presentationFormat);	×
72	} else {
73	setRespContentType(format);	9✔
74	}
75
76	if (req.matches("/(np\|get)/RA[a-zA-Z0-9-_]{43}(\\.[a-z]+)?")) {	12!
77	String ac = req.replaceFirst("/(np\|get)/(RA[a-zA-Z0-9-_]{43})(\\.[a-z]+)?", "$2");	15✔
78	Document npDoc = collection(Collection.NANOPUBS.toString()).find(new Document("_id", ac)).first();	36✔
79	if (npDoc == null) {	6✔
80	if (!isSet(mongoSession, Collection.SERVER_INFO.toString(), "testInstance")) {	21!
81	//getResp().sendError(404, "Not found: " + ac);
82	c.response().setStatusCode(307);	15✔
83	c.response().putHeader("Location", "https://np.knowledgepixels.com/" + ac);	21✔
84	return;	3✔
85	} else {
86	c.response().setStatusCode(404).setStatusMessage("Not found: " + getFullRequest());	×
87	return;	×
88	}
89	}
90	// String url = ServerConf.getInfo().getPublicUrl();
91	if (TYPE_TRIG.equals(format)) {	12✔
92	println(npDoc.getString("content"));	18✔
93	} else if (TYPE_JELLY.equals(format)) {	12!
94	if (presentationFormat != null && presentationFormat.startsWith("text")) {	×
95	// Parse the Jelly frame and return it as Protobuf Text Format Language
96	// https://protobuf.dev/reference/protobuf/textformat-spec/
97	// It's better than bombarding the browser with a binary file.
98	var frame = eu.neverblink.jelly.core.proto.google.v1.RdfStreamFrame	×
99	.parseFrom(((Binary) npDoc.get("jelly")).getData());	×
100	println(frame.toString());	×
101	} else {	×
102	// To return this correctly, we would need to prepend the delimiter byte before the Jelly frame
103	// (the DB stores is non-delimited and the HTTP response must be delimited).
104	BufferOutputStream outputStream = new BufferOutputStream();	×
105	IoUtils.writeFrameAsDelimited(	×
106	((Binary) npDoc.get("jelly")).getData(),	×
107	outputStream
108	);
109	c.response().write(outputStream.getBuffer());	×
110	}	×
111	} else if (format != null && format.equals(TYPE_NQUADS)) {	18!
112	outputNanopub(npDoc, RDFFormat.NQUADS);	×
113	} else if (format != null && format.equals(TYPE_JSONLD)) {	18!
114	outputNanopub(npDoc, RDFFormat.JSONLD);	×
115	} else if (format != null && format.equals(TYPE_TRIX)) {	18!
116	outputNanopub(npDoc, RDFFormat.TRIX);	×
117	} else if (forwardHtml && isHtmlRequested(c)) {	18✔
118	String fullId = npDoc.getString("fullId");	12✔
119	c.response().setStatusCode(302);	15✔
120	c.response().putHeader("Location", getNanodashBaseUrl() + "explore?id=" + Utils.urlEncode(fullId));	27✔
121	return;	3✔
122	} else if (forwardHtml) {	9✔
123	// Non-HTML default for /get/ path (e.g. Accept: /): serve as trig
124	setRespContentType(TYPE_TRIG);	9✔
125	println(npDoc.getString("content"));	18✔
126	} else {
127	printHtmlHeader("Nanopublication " + ac + " - Nanopub Registry");	12✔
128	println("<h1>Nanopublication</h1>");	9✔
129	println("<p><a href=\"/\">< Home</a></p>");	9✔
130	println("<h3>ID</h3>");	9✔
131	String fullId = npDoc.getString("fullId");	12✔
132	println("<p><a href=\"" + fullId + "\"><code>" + fullId + "</code></a></p>");	15✔
133	println("<h3>Formats</h3>");	9✔
134	println("<p>");	9✔
135	println("<a href=\"/np/" + ac + ".trig\">.trig</a> \|");	12✔
136	println("<a href=\"/np/" + ac + ".trig.txt\">.trig.txt</a> \|");	12✔
137	println("<a href=\"/np/" + ac + ".jelly\">.jelly</a> \|");	12✔
138	println("<a href=\"/np/" + ac + ".jelly.txt\">.jelly.txt</a> \|");	12✔
139	println("<a href=\"/np/" + ac + ".jsonld\">.jsonld</a> \|");	12✔
140	println("<a href=\"/np/" + ac + ".jsonld.txt\">.jsonld.txt</a> \|");	12✔
141	println("<a href=\"/np/" + ac + ".nq\">.nq</a> \|");	12✔
142	println("<a href=\"/np/" + ac + ".nq.txt\">.nq.txt</a> \|");	12✔
143	println("<a href=\"/np/" + ac + ".xml\">.xml</a> \|");	12✔
144	println("<a href=\"/np/" + ac + ".xml.txt\">.xml.txt</a>");	12✔
145	println("</p>");	9✔
146	println("<h3>Content</h3>");	9✔
147	println("<pre>");	9✔
148	println(StringEscapeUtils.escapeHtml(npDoc.getString("content")));	18✔
149	println("</pre>");	9✔
150	printHtmlFooter();	6✔
151	}
152	} else {	3✔
153	c.response().setStatusCode(400).setStatusMessage("Invalid request: " + getFullRequest());	×
154	}
155	}	3✔
156
157	private static boolean isHtmlRequested(RoutingContext c) {
158	String accept = c.request().getHeader("Accept");	15✔
159	return accept != null && accept.contains("text/html");	30!
160	}
161
162	private void outputNanopub(Document npDoc, RDFFormat rdfFormat) {
163	RoutingContext c = getContext();	×
164	try {
165	Nanopub np = new NanopubImpl(npDoc.getString("content"), RDFFormat.TRIG);	×
166	c.response().write(NanopubUtils.writeToString(np, rdfFormat), Charsets.UTF_8.toString());	×
167	} catch (RDF4JException \| MalformedNanopubException \| IOException ex) {	×
168	c.response().setStatusCode(500).setStatusMessage("Failed transforming nanopub: " + getFullRequest());	×
169	ex.printStackTrace();	×
170	}	×
171	}	×
172
173	}

knowledgepixels / nanopub-registry / 23243177209

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