19637760718

Committed 24 Nov 2025 02:27PM UTC coverage: 51.823% (-0.08%) from 51.902%

Build # 19637760718

Build Type

push

github

Committed by Ziroli Plutschow

Commit Message

Bring Cli-Option -v (Verbose) together with Logging

Little hack:
- We interpret an enabled DEBUG Log like the command line flag "verbose".
- The other way around, we do interpret the command line concept of setting the verbose flag as  activation of debug log.

TODO Issue: The verbose mode does not seem to work!

Run Details

1012 of 2922 branches covered (34.63%)

Branch coverage included in aggregate %.

5215 of 9094 relevant lines covered (57.35%)

2.69 hits per line

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82.52

src/main/java/org/nanopub/extra/services/QueryCall.java

package org.nanopub.extra.services;

import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;

import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.util.EntityUtils;
import org.nanopub.NanopubUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Second-generation query API call.
 */
public class QueryCall {

    private static int parallelCallCount = 2;
    private static int maxRetryCount = 3;
    private static final Logger logger = LoggerFactory.getLogger(QueryCall.class);

    /**
     * Run a query call with the given query ID and parameters.
     *
     * @param queryId the ID of the query to run
     * @param params  the parameters to pass to the query
     * @return the HTTP response from the query API
     */
    public static HttpResponse run(QueryRef queryRef) throws APINotReachableException, NotEnoughAPIInstancesException {
        int retryCount = 0;
        while (retryCount < maxRetryCount) {
            QueryCall apiCall = new QueryCall(queryRef);
            apiCall.run();
            while (!apiCall.calls.isEmpty() && apiCall.resp == null) {
                try {
                    Thread.sleep(200);
                } catch (InterruptedException ex) {
                    Thread.currentThread().interrupt();
                }
            }
            if (apiCall.resp != null) {
                return apiCall.resp;
            }
            retryCount = retryCount + 1;
        }
        throw new APINotReachableException("Giving up contacting API: " + queryRef.getName());
    }

    /**
     * List of available query API instances.
     */
    // TODO Available services should be retrieved from a setting, not hard-coded:
    public static String[] queryApiInstances = new String[]{
            "https://query.knowledgepixels.com/",
            "https://query.petapico.org/",
            "https://query.np.trustyuri.net/"
    };

    private static List<String> checkedApiInstances;

    /**
     * Returns the list of available query API instances that are currently accessible.
     *
     * @return a list of accessible query API instance
     */
    public static List<String> getApiInstances() throws NotEnoughAPIInstancesException {
        if (checkedApiInstances != null) return checkedApiInstances;
        checkedApiInstances = new ArrayList<>();
        for (String a : queryApiInstances) {
            try {
                logger.info("Checking API instance: {}", a);
                HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(a));
                if (wasSuccessful(resp)) {
                    logger.info("SUCCESS: Nanopub Query instance is accessible: {}", a);
                    checkedApiInstances.add(a);
                } else {
                    logger.error("FAILURE: Nanopub Query instance isn't accessible: {}", a);
                }
            } catch (IOException ex) {
                logger.error("FAILURE: Nanopub Query instance isn't accessible: {}", a);
            }
        }
        logger.info("{} accessible Nanopub Query instances", checkedApiInstances.size());
        if (checkedApiInstances.size() < 2) {
            checkedApiInstances = null;
            throw new NotEnoughAPIInstancesException("Not enough healthy Nanopub Query instances available");
        }
        return checkedApiInstances;
    }

    private QueryRef queryRef;
    private List<String> apisToCall = new ArrayList<>();
    private List<Call> calls = new ArrayList<>();

    private HttpResponse resp;

    private QueryCall(QueryRef queryRef) {
        this.queryRef = queryRef;
        logger.info("Invoking API operation {}", queryRef);
    }

    private void run() throws NotEnoughAPIInstancesException {
        List<String> apiInstancesToTry = new LinkedList<>(getApiInstances());
        while (!apiInstancesToTry.isEmpty() && apisToCall.size() < parallelCallCount) {
            int randomIndex = (int) ((Math.random() * apiInstancesToTry.size()));
            String apiUrl = apiInstancesToTry.get(randomIndex);
            apisToCall.add(apiUrl);
            logger.info("Trying API ({}) {}", apisToCall.size(), apiUrl);
            apiInstancesToTry.remove(randomIndex);
        }
        for (String api : apisToCall) {
            Call call = new Call(api);
            calls.add(call);
            new Thread(call).start();
        }
    }

    private synchronized void finished(Call call, HttpResponse resp, String apiUrl) {
        if (this.resp != null) { // result already in
            EntityUtils.consumeQuietly(resp.getEntity());
            return;
        }
        logger.info("Result in from {}:", apiUrl);
        logger.info("- Request: {}", queryRef);
        logger.info("- Response size: {}", resp.getEntity().getContentLength());
        this.resp = resp;

        for (Call c : calls) {
            if (c != call) c.abort();
        }
    }

    private static boolean wasSuccessful(HttpResponse resp) {
        if (resp == null || resp.getEntity() == null) return false;
        int c = resp.getStatusLine().getStatusCode();
        if (c < 200 || c >= 300) return false;
        return true;
    }

    private static boolean wasSuccessfulNonempty(HttpResponse resp) {
        if (!wasSuccessful(resp)) return false;
        // TODO Make sure we always return proper error codes, and then this shouldn't be necessary:
        if (resp.getHeaders("Content-Length").length > 0 && resp.getEntity().getContentLength() < 0) return false;
        return true;
    }


    private class Call implements Runnable {

        private String apiUrl;
        private HttpGet get;

        public Call(String apiUrl) {
            this.apiUrl = apiUrl;
        }

        public void run() {
            get = new HttpGet(apiUrl + "api/" + queryRef.getAsUrlString());
            get.setHeader("Accept", "text/csv");
            HttpResponse resp = null;
            try {
                resp = NanopubUtils.getHttpClient().execute(get);
                if (!wasSuccessfulNonempty(resp)) {
                    throw new IOException(resp.getStatusLine().toString());
                }
                finished(this, resp, apiUrl);
            } catch (Exception ex) {
                if (resp != null) EntityUtils.consumeQuietly(resp.getEntity());
                logger.error("Request to {} was not successful: {}", apiUrl, ex.getMessage());
            }
            calls.remove(this);
        }

        private void abort() {
            if (get == null) return;
            if (get.isAborted()) return;
            get.abort();
        }

    }

}

1	package org.nanopub.extra.services;
2
3	import java.io.IOException;
4	import java.util.ArrayList;
5	import java.util.LinkedList;
6	import java.util.List;
7
8	import org.apache.http.HttpResponse;
9	import org.apache.http.client.methods.HttpGet;
10	import org.apache.http.util.EntityUtils;
11	import org.nanopub.NanopubUtils;
12	import org.slf4j.Logger;
13	import org.slf4j.LoggerFactory;
14
15	/**
16	* Second-generation query API call.
17	*/
18	public class QueryCall {
19
20	private static int parallelCallCount = 2;	2✔
21	private static int maxRetryCount = 3;	2✔
22	private static final Logger logger = LoggerFactory.getLogger(QueryCall.class);	3✔
23
24	/**
25	* Run a query call with the given query ID and parameters.
26	*
27	* @param queryId the ID of the query to run
28	* @param params the parameters to pass to the query
29	* @return the HTTP response from the query API
30	*/
31	public static HttpResponse run(QueryRef queryRef) throws APINotReachableException, NotEnoughAPIInstancesException {
32	int retryCount = 0;	2✔
33	while (retryCount < maxRetryCount) {	3!
34	QueryCall apiCall = new QueryCall(queryRef);	5✔
35	apiCall.run();	2✔
36	while (!apiCall.calls.isEmpty() && apiCall.resp == null) {	7!
37	try {
38	Thread.sleep(200);	2✔
39	} catch (InterruptedException ex) {	×
40	Thread.currentThread().interrupt();	×
41	}	1✔
42	}
43	if (apiCall.resp != null) {	3!
44	return apiCall.resp;	3✔
45	}
46	retryCount = retryCount + 1;	×
47	}	×
48	throw new APINotReachableException("Giving up contacting API: " + queryRef.getName());	×
49	}
50
51	/**
52	* List of available query API instances.
53	*/
54	// TODO Available services should be retrieved from a setting, not hard-coded:
55	public static String[] queryApiInstances = new String[]{	16✔
56	"https://query.knowledgepixels.com/",
57	"https://query.petapico.org/",
58	"https://query.np.trustyuri.net/"
59	};
60
61	private static List<String> checkedApiInstances;
62
63	/**
64	* Returns the list of available query API instances that are currently accessible.
65	*
66	* @return a list of accessible query API instance
67	*/
68	public static List<String> getApiInstances() throws NotEnoughAPIInstancesException {
69	if (checkedApiInstances != null) return checkedApiInstances;	4✔
70	checkedApiInstances = new ArrayList<>();	4✔
71	for (String a : queryApiInstances) {	16✔
72	try {
73	logger.info("Checking API instance: {}", a);	4✔
74	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(a));	7✔
75	if (wasSuccessful(resp)) {	3✔
76	logger.info("SUCCESS: Nanopub Query instance is accessible: {}", a);	4✔
77	checkedApiInstances.add(a);	5✔
78	} else {
79	logger.error("FAILURE: Nanopub Query instance isn't accessible: {}", a);	4✔
80	}
81	} catch (IOException ex) {	×
82	logger.error("FAILURE: Nanopub Query instance isn't accessible: {}", a);	×
83	}	1✔
84	}
85	logger.info("{} accessible Nanopub Query instances", checkedApiInstances.size());	6✔
86	if (checkedApiInstances.size() < 2) {	4✔
87	checkedApiInstances = null;	2✔
88	throw new NotEnoughAPIInstancesException("Not enough healthy Nanopub Query instances available");	5✔
89	}
90	return checkedApiInstances;	2✔
91	}
92
93	private QueryRef queryRef;
94	private List<String> apisToCall = new ArrayList<>();	5✔
95	private List<Call> calls = new ArrayList<>();	5✔
96
97	private HttpResponse resp;
98
99	private QueryCall(QueryRef queryRef) {	2✔
100	this.queryRef = queryRef;	3✔
101	logger.info("Invoking API operation {}", queryRef);	4✔
102	}	1✔
103
104	private void run() throws NotEnoughAPIInstancesException {
105	List<String> apiInstancesToTry = new LinkedList<>(getApiInstances());	5✔
106	while (!apiInstancesToTry.isEmpty() && apisToCall.size() < parallelCallCount) {	8!
107	int randomIndex = (int) ((Math.random() * apiInstancesToTry.size()));	7✔
108	String apiUrl = apiInstancesToTry.get(randomIndex);	5✔
109	apisToCall.add(apiUrl);	5✔
110	logger.info("Trying API ({}) {}", apisToCall.size(), apiUrl);	8✔
111	apiInstancesToTry.remove(randomIndex);	4✔
112	}	1✔
113	for (String api : apisToCall) {	11✔
114	Call call = new Call(api);	6✔
115	calls.add(call);	5✔
116	new Thread(call).start();	5✔
117	}	1✔
118	}	1✔
119
120	private synchronized void finished(Call call, HttpResponse resp, String apiUrl) {
121	if (this.resp != null) { // result already in	3!
122	EntityUtils.consumeQuietly(resp.getEntity());	×
123	return;	×
124	}
125	logger.info("Result in from {}:", apiUrl);	4✔
126	logger.info("- Request: {}", queryRef);	5✔
127	logger.info("- Response size: {}", resp.getEntity().getContentLength());	7✔
128	this.resp = resp;	3✔
129
130	for (Call c : calls) {	11✔
131	if (c != call) c.abort();	5✔
132	}	1✔
133	}	1✔
134
135	private static boolean wasSuccessful(HttpResponse resp) {
136	if (resp == null \|\| resp.getEntity() == null) return false;	5!
137	int c = resp.getStatusLine().getStatusCode();	4✔
138	if (c < 200 \|\| c >= 300) return false;	8!
139	return true;	2✔
140	}
141
142	private static boolean wasSuccessfulNonempty(HttpResponse resp) {
143	if (!wasSuccessful(resp)) return false;	3!
144	// TODO Make sure we always return proper error codes, and then this shouldn't be necessary:
145	if (resp.getHeaders("Content-Length").length > 0 && resp.getEntity().getContentLength() < 0) return false;	11!
146	return true;	2✔
147	}
148
149
150	private class Call implements Runnable {
151
152	private String apiUrl;
153	private HttpGet get;
154
155	public Call(String apiUrl) {	5✔
156	this.apiUrl = apiUrl;	3✔
157	}	1✔
158
159	public void run() {
160	get = new HttpGet(apiUrl + "api/" + queryRef.getAsUrlString());	12✔
161	get.setHeader("Accept", "text/csv");	5✔
162	HttpResponse resp = null;	2✔
163	try {
164	resp = NanopubUtils.getHttpClient().execute(get);	5✔
165	if (!wasSuccessfulNonempty(resp)) {	3!
166	throw new IOException(resp.getStatusLine().toString());	×
167	}
168	finished(this, resp, apiUrl);	7✔
169	} catch (Exception ex) {	1✔
170	if (resp != null) EntityUtils.consumeQuietly(resp.getEntity());	2!
171	logger.error("Request to {} was not successful: {}", apiUrl, ex.getMessage());	7✔
172	}	1✔
173	calls.remove(this);	6✔
174	}	1✔
175
176	private void abort() {
177	if (get == null) return;	3!
178	if (get.isAborted()) return;	4!
179	get.abort();	3✔
180	}	1✔
181
182	}
183
184	}

Nanopublication / nanopub-java / 19637760718

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