17069388833

Committed 19 Aug 2025 12:21PM UTC coverage: 45.825% (-1.9%) from 47.675%

Build Type

push

github

Committed by Ziroli Plutschow

Commit Message

Fixed some TODOs

Run Details

825 of 2880 branches covered (28.65%)

Branch coverage included in aggregate %.

4603 of 8965 relevant lines covered (51.34%)

2.46 hits per line

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33.12

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

package org.nanopub.extra.services;

import org.apache.commons.codec.Charsets;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.util.EntityUtils;
import org.nanopub.NanopubUtils;

import java.io.IOException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;

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

    private static int parallelCallCount = 2;
    private static int maxRetryCount = 3;

    /**
     * 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(String queryId, Map<String, String> params) {
        int retryCount = 0;
        while (retryCount < maxRetryCount) {
            QueryCall apiCall = new QueryCall(queryId, params);
            apiCall.run();
            while (!apiCall.calls.isEmpty() && apiCall.resp == null) {
                try {
                    Thread.sleep(50);
                } catch (InterruptedException ex) {
                    Thread.currentThread().interrupt();
                }
            }
            if (apiCall.resp != null) {
                return apiCall.resp;
            }
            retryCount = retryCount + 1;
        }
        throw new RuntimeException("Giving up contacting API: " + queryId);
    }

    /**
     * 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() {
        if (checkedApiInstances != null) return checkedApiInstances;
        checkedApiInstances = new ArrayList<>();
        for (String a : queryApiInstances) {
            try {
                System.err.println("Checking API instance: " + a);
                HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(a));
                if (wasSuccessful(resp)) {
                    System.err.println("SUCCESS: Nanopub Query instance is accessible: " + a);
                    checkedApiInstances.add(a);
                } else {
                    System.err.println("FAILURE: Nanopub Query instance isn't accessible: " + a);
                }
            } catch (IOException ex) {
                System.err.println("FAILURE: Nanopub Query instance isn't accessible: " + a);
            }
        }
        System.err.println(checkedApiInstances.size() + " accessible Nanopub Query instances");
        if (checkedApiInstances.size() < 2) {
            checkedApiInstances = null;
            throw new RuntimeException("Not enough healthy Nanopub Query instances available");
        }
        return checkedApiInstances;
    }

    private String queryId;
    private String paramString;
    private List<String> apisToCall = new ArrayList<>();
    private List<Call> calls = new ArrayList<>();

    private HttpResponse resp;

    private QueryCall(String queryId, Map<String, String> params) {
        this.queryId = queryId;
        paramString = "";
        if (params != null) {
            paramString = "?";
            for (String k : params.keySet()) {
                if (paramString.length() > 1) paramString += "&";
                paramString += k + "=";
                paramString += URLEncoder.encode(params.get(k), Charsets.UTF_8);
            }
        }
        System.err.println("Invoking API operation " + queryId + " " + paramString);
    }

    private void run() {
        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);
            System.err.println("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;
        }
        System.err.println("Result in from " + apiUrl + ":");
        System.err.println("- Request: " + queryId + " " + paramString);
        System.err.println("- 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;
        if (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/" + queryId + paramString);
            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());
                System.err.println("Request to " + apiUrl + " was not successful: " + 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 org.apache.commons.codec.Charsets;
4	import org.apache.http.HttpResponse;
5	import org.apache.http.client.methods.HttpGet;
6	import org.apache.http.util.EntityUtils;
7	import org.nanopub.NanopubUtils;
8
9	import java.io.IOException;
10	import java.net.URLEncoder;
11	import java.util.ArrayList;
12	import java.util.LinkedList;
13	import java.util.List;
14	import java.util.Map;
15
16	/**
17	* Second-generation query API call.
18	*/
19	public class QueryCall {
20
21	private static int parallelCallCount = 2;	2✔
22	private static int maxRetryCount = 3;	2✔
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(String queryId, Map<String, String> params) {
32	int retryCount = 0;	2✔
33	while (retryCount < maxRetryCount) {	3!
34	QueryCall apiCall = new QueryCall(queryId, params);	×
35	apiCall.run();	×
36	while (!apiCall.calls.isEmpty() && apiCall.resp == null) {	×
37	try {
38	Thread.sleep(50);	×
39	} catch (InterruptedException ex) {	×
40	Thread.currentThread().interrupt();	×
41	}	×
42	}
43	if (apiCall.resp != null) {	×
44	return apiCall.resp;	×
45	}
46	retryCount = retryCount + 1;	×
47	}	×
48	throw new RuntimeException("Giving up contacting API: " + queryId);	×
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() {
69	if (checkedApiInstances != null) return checkedApiInstances;	4✔
70	checkedApiInstances = new ArrayList<>();	4✔
71	for (String a : queryApiInstances) {	16✔
72	try {
73	System.err.println("Checking API instance: " + a);	4✔
74	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(a));	7✔
75	if (wasSuccessful(resp)) {	3✔
76	System.err.println("SUCCESS: Nanopub Query instance is accessible: " + a);	4✔
77	checkedApiInstances.add(a);	5✔
78	} else {
79	System.err.println("FAILURE: Nanopub Query instance isn't accessible: " + a);	4✔
80	}
81	} catch (IOException ex) {	×
82	System.err.println("FAILURE: Nanopub Query instance isn't accessible: " + a);	×
83	}	1✔
84	}
85	System.err.println(checkedApiInstances.size() + " accessible Nanopub Query instances");	5✔
86	if (checkedApiInstances.size() < 2) {	4✔
87	checkedApiInstances = null;	2✔
88	throw new RuntimeException("Not enough healthy Nanopub Query instances available");	5✔
89	}
90	return checkedApiInstances;	2✔
91	}
92
93	private String queryId;
94	private String paramString;
95	private List<String> apisToCall = new ArrayList<>();	5✔
96	private List<Call> calls = new ArrayList<>();	5✔
97
98	private HttpResponse resp;
99
100	private QueryCall(String queryId, Map<String, String> params) {	2✔
101	this.queryId = queryId;	3✔
102	paramString = "";	3✔
103	if (params != null) {	2!
104	paramString = "?";	3✔
105	for (String k : params.keySet()) {	11!
106	if (paramString.length() > 1) paramString += "&";	5!
107	paramString += k + "=";	6✔
108	paramString += URLEncoder.encode(params.get(k), Charsets.UTF_8);	×
109	}	×
110	}
111	System.err.println("Invoking API operation " + queryId + " " + paramString);	×
112	}	×
113
114	private void run() {
115	List<String> apiInstancesToTry = new LinkedList<>(getApiInstances());	×
116	while (!apiInstancesToTry.isEmpty() && apisToCall.size() < parallelCallCount) {	×
117	int randomIndex = (int) ((Math.random() * apiInstancesToTry.size()));	×
118	String apiUrl = apiInstancesToTry.get(randomIndex);	×
119	apisToCall.add(apiUrl);	×
120	System.err.println("Trying API (" + apisToCall.size() + ") " + apiUrl);	×
121	apiInstancesToTry.remove(randomIndex);	×
122	}	×
123	for (String api : apisToCall) {	×
124	Call call = new Call(api);	×
125	calls.add(call);	×
126	new Thread(call).start();	×
127	}	×
128	}	×
129
130	private synchronized void finished(Call call, HttpResponse resp, String apiUrl) {
131	if (this.resp != null) { // result already in	×
132	EntityUtils.consumeQuietly(resp.getEntity());	×
133	return;	×
134	}
135	System.err.println("Result in from " + apiUrl + ":");	×
136	System.err.println("- Request: " + queryId + " " + paramString);	×
137	System.err.println("- Response size: " + resp.getEntity().getContentLength());	×
138	this.resp = resp;	×
139
140	for (Call c : calls) {	×
141	if (c != call) c.abort();	×
142	}	×
143	}	×
144
145	private static boolean wasSuccessful(HttpResponse resp) {
146	if (resp == null \|\| resp.getEntity() == null) return false;	5!
147	int c = resp.getStatusLine().getStatusCode();	4✔
148	if (c < 200 \|\| c >= 300) return false;	8!
149	return true;	2✔
150	}
151
152	private static boolean wasSuccessfulNonempty(HttpResponse resp) {
153	if (!wasSuccessful(resp)) return false;	×
154	if (resp.getEntity().getContentLength() < 0) return false;	×
155	return true;	×
156	}
157
158
159	private class Call implements Runnable {
160
161	private String apiUrl;
162	private HttpGet get;
163
164	public Call(String apiUrl) {	×
165	this.apiUrl = apiUrl;	×
166	}	×
167
168	public void run() {
169	get = new HttpGet(apiUrl + "api/" + queryId + paramString);	×
170	get.setHeader("Accept", "text/csv");	×
171	HttpResponse resp = null;	×
172	try {
173	resp = NanopubUtils.getHttpClient().execute(get);	×
174	if (!wasSuccessfulNonempty(resp)) {	×
175	throw new IOException(resp.getStatusLine().toString());	×
176	}
177	finished(this, resp, apiUrl);	×
178	} catch (Exception ex) {	×
179	if (resp != null) EntityUtils.consumeQuietly(resp.getEntity());	×
180	System.err.println("Request to " + apiUrl + " was not successful: " + ex.getMessage());	×
181	}	×
182	calls.remove(this);	×
183	}	×
184
185	private void abort() {
186	if (get == null) return;	×
187	if (get.isAborted()) return;	×
188	get.abort();	×
189	}	×
190
191	}
192
193	}

Nanopublication / nanopub-java / 17069388833

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