24139339422

Committed 08 Apr 2026 01:58PM UTC coverage: 32.357% (-0.5%) from 32.824%

Build # 24139339422

Build Type

Pull #98

github

Committed by

web-flow

Commit Message

Merge f359f2357 into 689a63b39

Pull Request Pull Request #98: Revert seqNum batch allocation, use atomic counter

Coverage Stats

265 of 916 branches covered (28.93%)

Branch coverage included in aggregate %.

785 of 2329 relevant lines covered (33.71%)

5.66 hits per line

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92.47

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

package com.knowledgepixels.registry;

import com.mongodb.client.ClientSession;
import org.bson.Document;
import io.vertx.core.http.HttpMethod;
import io.vertx.ext.web.RoutingContext;
import org.apache.commons.lang.StringEscapeUtils;

import java.io.IOException;
import java.text.DecimalFormat;

import static com.knowledgepixels.registry.RegistryDB.*;

public abstract class Page {

    protected static final DecimalFormat df8 = new DecimalFormat("0.00000000");
    protected static final DecimalFormat df1 = new DecimalFormat("0.0");

    private RoutingContext context;
    protected ClientSession mongoSession;
    protected Document serverInfo;

    private String presentationFormat;
    private String extension;
    private String requestString;

    /**
     * Constructor for the Page class.
     *
     * @param mongoSession The MongoDB client session.
     * @param context      The routing context.
     */
    public Page(ClientSession mongoSession, RoutingContext context) {
        this.mongoSession = mongoSession;
        this.context = context;
        context.response().setChunked(true);

        // Fetch all serverInfo key-value pairs in one query instead of separate getValue calls
        serverInfo = new Document();
        for (Document d : collection(Collection.SERVER_INFO.toString()).find(mongoSession)) {
            serverInfo.put(d.getString("_id"), d.get("value"));
        }
        context.response().putHeader("Nanopub-Registry-Status", serverInfo.get("status") + "");
        context.response().putHeader("Nanopub-Registry-Setup-Id", serverInfo.get("setupId") + "");
        context.response().putHeader("Nanopub-Registry-Trust-State-Counter", serverInfo.get("trustStateCounter") + "");
        context.response().putHeader("Nanopub-Registry-Last-Trust-State-Update", serverInfo.get("lastTrustStateUpdate") + "");
        context.response().putHeader("Nanopub-Registry-Trust-State-Hash", serverInfo.get("trustStateHash") + "");
        Object maxCounter = getMaxValue(mongoSession, Collection.NANOPUBS.toString(), "counter");
        context.response().putHeader("Nanopub-Registry-Load-Counter", maxCounter + "");
        context.response().putHeader("Nanopub-Registry-Nanopub-Count", collection(Collection.NANOPUBS.toString()).estimatedDocumentCount() + "");
        context.response().putHeader("Nanopub-Registry-Test-Instance", String.valueOf(serverInfo.get("testInstance") != null && (Boolean) serverInfo.get("testInstance")));
        context.response().putHeader("Nanopub-Registry-Coverage-Types", serverInfo.get("coverageTypes") != null ? serverInfo.get("coverageTypes").toString() : "all");
        context.response().putHeader("Nanopub-Registry-Coverage-Agents", serverInfo.get("coverageAgents") != null ? serverInfo.get("coverageAgents").toString() : "viaSetting");

        String r = context.request().path().substring(1);
        if (r.endsWith(".txt")) {
            presentationFormat = "text/plain";
            r = r.replaceFirst("\\.txt$", "");
        } else if (r.endsWith(".html")) {
            presentationFormat = "text/html";
            r = r.replaceFirst("\\.html$", "");
//                } else if (r.endsWith(".gz")) {
//                        presentationFormat = "application/x-gzip";
//                        r = r.replaceFirst("\\.gz$", "");
        }
        if (r.matches(".*\\.[a-z]{1,10}")) {
            extension = r.replaceFirst("^.*\\.([a-z]{1,10})$", "$1");
            requestString = r.replaceFirst("^(.*)\\.[a-z]{1,10}$", "$1");
        } else {
            requestString = r;
        }
    }

    /**
     * Get the routing context.
     *
     * @return The routing context.
     */
    public RoutingContext getContext() {
        return context;
    }

    /**
     * Print a line to the response.
     *
     * @param s The string to print.
     */
    public void println(String s) {
        print(s + "\n");
    }

    /**
     * Print a string to the response.
     *
     * @param s The string to print.
     */
    public void print(String s) {
        if (context.request().method() == HttpMethod.HEAD) {
            return;
        }
        context.response().write(s);
    }

    /**
     * Set the response content type.
     *
     * @param contentType The content type.
     */
    public void setRespContentType(String contentType) {
        if (context.request().method() == HttpMethod.HEAD) {
            return;
        }
        context.response().putHeader("Content-Type", contentType);
    }

    /**
     * Show the page.
     *
     * @throws IOException
     */
    protected abstract void show() throws IOException;

    /**
     * Print the HTML header.
     *
     * @param title The title of the page.
     */
    public void printHtmlHeader(String title) {
        println("<!DOCTYPE HTML>");
        println("<html><head>");
        println("<title>" + title + "</title>");
        println("<meta charset=\"utf-8\"/>");
        println("<script type=\"text/javascript\" src=\"/scripts/nanopub.js\"></script>");
        println("<link rel=\"stylesheet\" href=\"/style.css\" type=\"text/css\" media=\"screen\" title=\"Stylesheet\" />");
        println("</head><body>");
    }

    /**
     * Print the HTML footer.
     */
    public void printHtmlFooter() {
        println("</body></html>");
    }

    /**
     * Escape HTML special characters in a string.
     *
     * @param text The text to escape.
     * @return The escaped text.
     */
    public String escapeHtml(String text) {
        return StringEscapeUtils.escapeHtml(text);
    }

    /**
     * Set the canonical link for this page.
     *
     * @param url The canonical URL.
     */
    public void setCanonicalLink(String url) {
        context.response().putHeader("Link", "<" + url + ">; rel=\"canonical\"");
    }

    /**
     * Get the presentation format requested, if any.
     *
     * @return The presentation format.
     */
    public String getPresentationFormat() {
        return presentationFormat;
    }

    /**
     * Get the extension requested, if any.
     *
     * @return The extension.
     */
    public String getExtension() {
        return extension;
    }

    /**
     * Get the request string with the leading slash and without extension.
     *
     * @return The request string.
     */
    public String getRequestString() {
        return "/" + requestString;
    }

    /**
     * Get the full request path.
     *
     * @return The full request path.
     */
    public String getFullRequest() {
        return context.request().path();
    }

    /**
     * Get a parameter from the request.
     *
     * @param name         The name of the parameter.
     * @param defaultValue The default value of the parameter.
     * @return The value of the parameter.
     */
    public String getParam(String name, String defaultValue) {
        String value = context.request().getParam(name);
        if (value == null) value = defaultValue;
        return value;
    }

    /**
     * Check whether the request is empty.
     *
     * @return True if the request is empty, false otherwise.
     */
    public boolean isEmpty() {
        return requestString.isEmpty();
    }

    /**
     * Check whether the request contains an artifact code.
     *
     * @return True if the request contains an artifact code, false otherwise.
     */
    public boolean hasArtifactCode() {
        return requestString.matches("RA[A-Za-z0-9\\-_]{43}");
    }

    /**
     * Get the artifact code from the request, if present.
     *
     * @return The artifact code, or null if not present.
     */
    public String getArtifactCode() {
        if (hasArtifactCode()) {
            return requestString;
        }
        return null;
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.mongodb.client.ClientSession;
4	import org.bson.Document;
5	import io.vertx.core.http.HttpMethod;
6	import io.vertx.ext.web.RoutingContext;
7	import org.apache.commons.lang.StringEscapeUtils;
8
9	import java.io.IOException;
10	import java.text.DecimalFormat;
11
12	import static com.knowledgepixels.registry.RegistryDB.*;
13
14	public abstract class Page {
15
16	protected static final DecimalFormat df8 = new DecimalFormat("0.00000000");	15✔
17	protected static final DecimalFormat df1 = new DecimalFormat("0.0");	18✔
18
19	private RoutingContext context;
20	protected ClientSession mongoSession;
21	protected Document serverInfo;
22
23	private String presentationFormat;
24	private String extension;
25	private String requestString;
26
27	/**
28	* Constructor for the Page class.
29	*
30	* @param mongoSession The MongoDB client session.
31	* @param context The routing context.
32	*/
33	public Page(ClientSession mongoSession, RoutingContext context) {	6✔
34	this.mongoSession = mongoSession;	9✔
35	this.context = context;	9✔
36	context.response().setChunked(true);	15✔
37
38	// Fetch all serverInfo key-value pairs in one query instead of separate getValue calls
39	serverInfo = new Document();	15✔
40	for (Document d : collection(Collection.SERVER_INFO.toString()).find(mongoSession)) {	42✔
41	serverInfo.put(d.getString("_id"), d.get("value"));	30✔
42	}	3✔
43	context.response().putHeader("Nanopub-Registry-Status", serverInfo.get("status") + "");	33✔
44	context.response().putHeader("Nanopub-Registry-Setup-Id", serverInfo.get("setupId") + "");	33✔
45	context.response().putHeader("Nanopub-Registry-Trust-State-Counter", serverInfo.get("trustStateCounter") + "");	33✔
46	context.response().putHeader("Nanopub-Registry-Last-Trust-State-Update", serverInfo.get("lastTrustStateUpdate") + "");	33✔
47	context.response().putHeader("Nanopub-Registry-Trust-State-Hash", serverInfo.get("trustStateHash") + "");	33✔
48	Object maxCounter = getMaxValue(mongoSession, Collection.NANOPUBS.toString(), "counter");	18✔
49	context.response().putHeader("Nanopub-Registry-Load-Counter", maxCounter + "");	24✔
50	context.response().putHeader("Nanopub-Registry-Nanopub-Count", collection(Collection.NANOPUBS.toString()).estimatedDocumentCount() + "");	30✔
51	context.response().putHeader("Nanopub-Registry-Test-Instance", String.valueOf(serverInfo.get("testInstance") != null && (Boolean) serverInfo.get("testInstance")));	57!
52	context.response().putHeader("Nanopub-Registry-Coverage-Types", serverInfo.get("coverageTypes") != null ? serverInfo.get("coverageTypes").toString() : "all");	33!
53	context.response().putHeader("Nanopub-Registry-Coverage-Agents", serverInfo.get("coverageAgents") != null ? serverInfo.get("coverageAgents").toString() : "viaSetting");	33!
54
55	String r = context.request().path().substring(1);	18✔
56	if (r.endsWith(".txt")) {	12✔
57	presentationFormat = "text/plain";	9✔
58	r = r.replaceFirst("\\.txt$", "");	18✔
59	} else if (r.endsWith(".html")) {	12✔
60	presentationFormat = "text/html";	9✔
61	r = r.replaceFirst("\\.html$", "");	15✔
62	// } else if (r.endsWith(".gz")) {
63	// presentationFormat = "application/x-gzip";
64	// r = r.replaceFirst("\\.gz$", "");
65	}
66	if (r.matches(".*\\.[a-z]{1,10}")) {	12✔
67	extension = r.replaceFirst("^.*\\.([a-z]{1,10})$", "$1");	18✔
68	requestString = r.replaceFirst("^(.*)\\.[a-z]{1,10}$", "$1");	21✔
69	} else {
70	requestString = r;	9✔
71	}
72	}	3✔
73
74	/**
75	* Get the routing context.
76	*
77	* @return The routing context.
78	*/
79	public RoutingContext getContext() {
80	return context;	9✔
81	}
82
83	/**
84	* Print a line to the response.
85	*
86	* @param s The string to print.
87	*/
88	public void println(String s) {
89	print(s + "\n");	12✔
90	}	3✔
91
92	/**
93	* Print a string to the response.
94	*
95	* @param s The string to print.
96	*/
97	public void print(String s) {
98	if (context.request().method() == HttpMethod.HEAD) {	18!
99	return;	×
100	}
101	context.response().write(s);	18✔
102	}	3✔
103
104	/**
105	* Set the response content type.
106	*
107	* @param contentType The content type.
108	*/
109	public void setRespContentType(String contentType) {
110	if (context.request().method() == HttpMethod.HEAD) {	18✔
111	return;	3✔
112	}
113	context.response().putHeader("Content-Type", contentType);	21✔
114	}	3✔
115
116	/**
117	* Show the page.
118	*
119	* @throws IOException
120	*/
121	protected abstract void show() throws IOException;
122
123	/**
124	* Print the HTML header.
125	*
126	* @param title The title of the page.
127	*/
128	public void printHtmlHeader(String title) {
129	println("<!DOCTYPE HTML>");	9✔
130	println("<html><head>");	9✔
131	println("<title>" + title + "</title>");	12✔
132	println("<meta charset=\"utf-8\"/>");	9✔
133	println("<script type=\"text/javascript\" src=\"/scripts/nanopub.js\"></script>");	9✔
134	println("<link rel=\"stylesheet\" href=\"/style.css\" type=\"text/css\" media=\"screen\" title=\"Stylesheet\" />");	9✔
135	println("</head><body>");	9✔
136	}	3✔
137
138	/**
139	* Print the HTML footer.
140	*/
141	public void printHtmlFooter() {
142	println("</body></html>");	9✔
143	}	3✔
144
145	/**
146	* Escape HTML special characters in a string.
147	*
148	* @param text The text to escape.
149	* @return The escaped text.
150	*/
151	public String escapeHtml(String text) {
152	return StringEscapeUtils.escapeHtml(text);	×
153	}
154
155	/**
156	* Set the canonical link for this page.
157	*
158	* @param url The canonical URL.
159	*/
160	public void setCanonicalLink(String url) {
161	context.response().putHeader("Link", "<" + url + ">; rel=\"canonical\"");	24✔
162	}	3✔
163
164	/**
165	* Get the presentation format requested, if any.
166	*
167	* @return The presentation format.
168	*/
169	public String getPresentationFormat() {
170	return presentationFormat;	9✔
171	}
172
173	/**
174	* Get the extension requested, if any.
175	*
176	* @return The extension.
177	*/
178	public String getExtension() {
179	return extension;	9✔
180	}
181
182	/**
183	* Get the request string with the leading slash and without extension.
184	*
185	* @return The request string.
186	*/
187	public String getRequestString() {
188	return "/" + requestString;	12✔
189	}
190
191	/**
192	* Get the full request path.
193	*
194	* @return The full request path.
195	*/
196	public String getFullRequest() {
197	return context.request().path();	15✔
198	}
199
200	/**
201	* Get a parameter from the request.
202	*
203	* @param name The name of the parameter.
204	* @param defaultValue The default value of the parameter.
205	* @return The value of the parameter.
206	*/
207	public String getParam(String name, String defaultValue) {
208	String value = context.request().getParam(name);	18✔
209	if (value == null) value = defaultValue;	12✔
210	return value;	6✔
211	}
212
213	/**
214	* Check whether the request is empty.
215	*
216	* @return True if the request is empty, false otherwise.
217	*/
218	public boolean isEmpty() {
219	return requestString.isEmpty();	12✔
220	}
221
222	/**
223	* Check whether the request contains an artifact code.
224	*
225	* @return True if the request contains an artifact code, false otherwise.
226	*/
227	public boolean hasArtifactCode() {
228	return requestString.matches("RA[A-Za-z0-9\\-_]{43}");	15✔
229	}
230
231	/**
232	* Get the artifact code from the request, if present.
233	*
234	* @return The artifact code, or null if not present.
235	*/
236	public String getArtifactCode() {
237	if (hasArtifactCode()) {	9✔
238	return requestString;	9✔
239	}
240	return null;	6✔
241	}
242
243	}

knowledgepixels / nanopub-registry / 24139339422

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