28113618611

Committed 24 Jun 2026 04:28PM UTC coverage: 31.926% (-0.2%) from 32.089%

Build # 28113618611

Build Type

Pull #116

github

Committed by

web-flow

Commit Message

Merge d931f8afc into eebd16ba4

Pull Request Pull Request #116: Enhance and standardize logging across multiple components

Coverage Stats

313 of 1106 branches covered (28.3%)

Branch coverage included in aggregate %.

1048 of 3157 relevant lines covered (33.2%)

5.51 hits per line

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89.72

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

package com.knowledgepixels.registry;

import com.mongodb.client.ClientSession;
import io.vertx.core.http.HttpMethod;
import io.vertx.ext.web.RoutingContext;
import org.apache.commons.lang.StringEscapeUtils;
import org.bson.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

import static com.knowledgepixels.registry.RegistryDB.collection;
import static com.knowledgepixels.registry.RegistryDB.getMaxValue;

public abstract class Page {

    private static final Logger logger = LoggerFactory.getLogger(Page.class);

    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-Version", Utils.getVersion());
        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;
        }

        logger.debug("Initialized Page for path={} requestString={} extension={} presentationFormat={}",
                context.request().path(), requestString, extension, presentationFormat);
        if (serverInfo.get("setupId") == null || serverInfo.get("status") == null) {
            logger.warn("Server info incomplete for request {}: setupId={} status={}", getFullRequest(), serverInfo.get("setupId"), serverInfo.get("status"));
        }
    }

    /**
     * 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) {
            logger.debug("Suppressing response body for HEAD request: {}", context.request().path());
            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) {
            logger.debug("Suppressing Content-Type header for HEAD request: {}", context.request().path());
            return;
        }
        context.response().putHeader("Content-Type", contentType);
        logger.debug("Set Content-Type={} for request={}", contentType, context.request().path());
    }

    /**
     * Show the page.
     *
     * @throws IOException If an I/O error occurs while showing the page.
     */
    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 io.vertx.core.http.HttpMethod;
5	import io.vertx.ext.web.RoutingContext;
6	import org.apache.commons.lang.StringEscapeUtils;
7	import org.bson.Document;
8	import org.slf4j.Logger;
9	import org.slf4j.LoggerFactory;
10
11	import java.io.IOException;
12	import java.text.DecimalFormat;
13
14	import static com.knowledgepixels.registry.RegistryDB.collection;
15	import static com.knowledgepixels.registry.RegistryDB.getMaxValue;
16
17	public abstract class Page {
18
19	private static final Logger logger = LoggerFactory.getLogger(Page.class);	9✔
20
21	protected static final DecimalFormat df8 = new DecimalFormat("0.00000000");	15✔
22	protected static final DecimalFormat df1 = new DecimalFormat("0.0");	18✔
23
24	private RoutingContext context;
25	protected ClientSession mongoSession;
26	protected Document serverInfo;
27
28	private String presentationFormat;
29	private String extension;
30	private String requestString;
31
32	/**
33	* Constructor for the Page class.
34	*
35	* @param mongoSession The MongoDB client session.
36	* @param context The routing context.
37	*/
38	public Page(ClientSession mongoSession, RoutingContext context) {	6✔
39	this.mongoSession = mongoSession;	9✔
40	this.context = context;	9✔
41	context.response().setChunked(true);	15✔
42
43	// Fetch all serverInfo key-value pairs in one query instead of separate getValue calls
44	serverInfo = new Document();	15✔
45	for (Document d : collection(Collection.SERVER_INFO.toString()).find(mongoSession)) {	42✔
46	serverInfo.put(d.getString("_id"), d.get("value"));	30✔
47	}	3✔
48	context.response().putHeader("Nanopub-Registry-Version", Utils.getVersion());	18✔
49	context.response().putHeader("Nanopub-Registry-Status", serverInfo.get("status") + "");	33✔
50	context.response().putHeader("Nanopub-Registry-Setup-Id", serverInfo.get("setupId") + "");	33✔
51	context.response().putHeader("Nanopub-Registry-Trust-State-Counter", serverInfo.get("trustStateCounter") + "");	33✔
52	context.response().putHeader("Nanopub-Registry-Last-Trust-State-Update", serverInfo.get("lastTrustStateUpdate") + "");	33✔
53	context.response().putHeader("Nanopub-Registry-Trust-State-Hash", serverInfo.get("trustStateHash") + "");	33✔
54	Object maxCounter = getMaxValue(mongoSession, Collection.NANOPUBS.toString(), "counter");	18✔
55	context.response().putHeader("Nanopub-Registry-Load-Counter", maxCounter + "");	24✔
56	context.response().putHeader("Nanopub-Registry-Nanopub-Count", collection(Collection.NANOPUBS.toString()).estimatedDocumentCount() + "");	30✔
57	context.response().putHeader("Nanopub-Registry-Test-Instance", String.valueOf(serverInfo.get("testInstance") != null && (Boolean) serverInfo.get("testInstance")));	57!
58	context.response().putHeader("Nanopub-Registry-Coverage-Types", serverInfo.get("coverageTypes") != null ? serverInfo.get("coverageTypes").toString() : "all");	33!
59	context.response().putHeader("Nanopub-Registry-Coverage-Agents", serverInfo.get("coverageAgents") != null ? serverInfo.get("coverageAgents").toString() : "viaSetting");	33!
60
61	String r = context.request().path().substring(1);	18✔
62	if (r.endsWith(".txt")) {	12✔
63	presentationFormat = "text/plain";	9✔
64	r = r.replaceFirst("\\.txt$", "");	18✔
65	} else if (r.endsWith(".html")) {	12✔
66	presentationFormat = "text/html";	9✔
67	r = r.replaceFirst("\\.html$", "");	15✔
68	// } else if (r.endsWith(".gz")) {
69	// presentationFormat = "application/x-gzip";
70	// r = r.replaceFirst("\\.gz$", "");
71	}
72	if (r.matches(".*\\.[a-z]{1,10}")) {	12✔
73	extension = r.replaceFirst("^.*\\.([a-z]{1,10})$", "$1");	18✔
74	requestString = r.replaceFirst("^(.*)\\.[a-z]{1,10}$", "$1");	21✔
75	} else {
76	requestString = r;	9✔
77	}
78
79	logger.debug("Initialized Page for path={} requestString={} extension={} presentationFormat={}",	24✔
80	context.request().path(), requestString, extension, presentationFormat);	54✔
81	if (serverInfo.get("setupId") == null \|\| serverInfo.get("status") == null) {	30!
82	logger.warn("Server info incomplete for request {}: setupId={} status={}", getFullRequest(), serverInfo.get("setupId"), serverInfo.get("status"));	×
83	}
84	}	3✔
85
86	/**
87	* Get the routing context.
88	*
89	* @return The routing context.
90	*/
91	public RoutingContext getContext() {
92	return context;	9✔
93	}
94
95	/**
96	* Print a line to the response.
97	*
98	* @param s The string to print.
99	*/
100	public void println(String s) {
101	print(s + "\n");	12✔
102	}	3✔
103
104	/**
105	* Print a string to the response.
106	*
107	* @param s The string to print.
108	*/
109	public void print(String s) {
110	if (context.request().method() == HttpMethod.HEAD) {	18!
111	logger.debug("Suppressing response body for HEAD request: {}", context.request().path());	×
112	return;	×
113	}
114	context.response().write(s);	18✔
115	}	3✔
116
117	/**
118	* Set the response content type.
119	*
120	* @param contentType The content type.
121	*/
122	public void setRespContentType(String contentType) {
123	if (context.request().method() == HttpMethod.HEAD) {	18✔
124	logger.debug("Suppressing Content-Type header for HEAD request: {}", context.request().path());	21✔
125	return;	3✔
126	}
127	context.response().putHeader("Content-Type", contentType);	21✔
128	logger.debug("Set Content-Type={} for request={}", contentType, context.request().path());	24✔
129	}	3✔
130
131	/**
132	* Show the page.
133	*
134	* @throws IOException If an I/O error occurs while showing the page.
135	*/
136	protected abstract void show() throws IOException;
137
138	/**
139	* Print the HTML header.
140	*
141	* @param title The title of the page.
142	*/
143	public void printHtmlHeader(String title) {
144	println("<!DOCTYPE HTML>");	9✔
145	println("<html><head>");	9✔
146	println("<title>" + title + "</title>");	12✔
147	println("<meta charset=\"utf-8\"/>");	9✔
148	println("<script type=\"text/javascript\" src=\"/scripts/nanopub.js\"></script>");	9✔
149	println("<link rel=\"stylesheet\" href=\"/style.css\" type=\"text/css\" media=\"screen\" title=\"Stylesheet\" />");	9✔
150	println("</head><body>");	9✔
151	}	3✔
152
153	/**
154	* Print the HTML footer.
155	*/
156	public void printHtmlFooter() {
157	println("</body></html>");	9✔
158	}	3✔
159
160	/**
161	* Escape HTML special characters in a string.
162	*
163	* @param text The text to escape.
164	* @return The escaped text.
165	*/
166	public String escapeHtml(String text) {
167	return StringEscapeUtils.escapeHtml(text);	×
168	}
169
170	/**
171	* Set the canonical link for this page.
172	*
173	* @param url The canonical URL.
174	*/
175	public void setCanonicalLink(String url) {
176	context.response().putHeader("Link", "<" + url + ">; rel=\"canonical\"");	24✔
177	}	3✔
178
179	/**
180	* Get the presentation format requested, if any.
181	*
182	* @return The presentation format.
183	*/
184	public String getPresentationFormat() {
185	return presentationFormat;	9✔
186	}
187
188	/**
189	* Get the extension requested, if any.
190	*
191	* @return The extension.
192	*/
193	public String getExtension() {
194	return extension;	9✔
195	}
196
197	/**
198	* Get the request string with the leading slash and without extension.
199	*
200	* @return The request string.
201	*/
202	public String getRequestString() {
203	return "/" + requestString;	12✔
204	}
205
206	/**
207	* Get the full request path.
208	*
209	* @return The full request path.
210	*/
211	public String getFullRequest() {
212	return context.request().path();	15✔
213	}
214
215	/**
216	* Get a parameter from the request.
217	*
218	* @param name The name of the parameter.
219	* @param defaultValue The default value of the parameter.
220	* @return The value of the parameter.
221	*/
222	public String getParam(String name, String defaultValue) {
223	String value = context.request().getParam(name);	18✔
224	if (value == null) {	6✔
225	value = defaultValue;	6✔
226	}
227	return value;	6✔
228	}
229
230	/**
231	* Check whether the request is empty.
232	*
233	* @return True if the request is empty, false otherwise.
234	*/
235	public boolean isEmpty() {
236	return requestString.isEmpty();	12✔
237	}
238
239	/**
240	* Check whether the request contains an artifact code.
241	*
242	* @return True if the request contains an artifact code, false otherwise.
243	*/
244	public boolean hasArtifactCode() {
245	return requestString.matches("RA[A-Za-z0-9\\-_]{43}");	15✔
246	}
247
248	/**
249	* Get the artifact code from the request, if present.
250	*
251	* @return The artifact code, or null if not present.
252	*/
253	public String getArtifactCode() {
254	if (hasArtifactCode()) {	9✔
255	return requestString;	9✔
256	}
257	return null;	6✔
258	}
259
260	}

knowledgepixels / nanopub-registry / 28113618611

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