19897067550

Committed 03 Dec 2025 02:19PM UTC coverage: 51.868% (+0.1%) from 51.73%

Build # 19897067550

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: remove unused code and update wrong javadoc annotations

Run Details

1013 of 2922 branches covered (34.67%)

Branch coverage included in aggregate %.

5221 of 9097 relevant lines covered (57.39%)

2.69 hits per line

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57.14

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

package org.nanopub.extra.services;

import com.opencsv.CSVReader;
import com.opencsv.CSVWriterBuilder;
import com.opencsv.ICSVWriter;
import com.opencsv.exceptions.CsvValidationException;
import org.apache.http.HttpResponse;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Writer;

/**
 * Second-generation query API access
 */
public abstract class QueryAccess {

    /**
     * Process the header.
     *
     * @param line the header line from the CSV response
     */
    protected abstract void processHeader(String[] line);

    /**
     * Process a line of data from the CSV response.
     *
     * @param line the line of data from the CSV response
     */
    protected abstract void processLine(String[] line);

    /**
     * Call a query with the given queryId and parameters.
     *
     * @param queryRef the query reference
     * @throws FailedApiCallException         if the API call fails
     * @throws APINotReachableException       if the API is not reachable
     * @throws NotEnoughAPIInstancesException if there are not enough API instances available
     */
    public void call(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
        HttpResponse resp = QueryCall.run(queryRef);
        try (CSVReader csvReader = new CSVReader(new BufferedReader(new InputStreamReader(resp.getEntity().getContent())))) {
            String[] line = null;
            int n = 0;
            while ((line = csvReader.readNext()) != null) {
                n++;
                if (n == 1) {
                    processHeader(line);
                } else {
                    processLine(line);
                }
            }
        } catch (IOException | CsvValidationException ex) {
            throw new FailedApiCallException(ex);
        }
    }

    /**
     * Print the response of a query in CSV format to the given writer.
     *
     * @param queryRef the query reference
     * @param writer   the writer to print the CSV response to
     * @throws FailedApiCallException         if the API call fails
     * @throws APINotReachableException       if the API is not reachable
     * @throws NotEnoughAPIInstancesException if there are not enough API instances available
     */
    public static void printCvsResponse(QueryRef queryRef, Writer writer) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
        ICSVWriter icsvWriter = new CSVWriterBuilder(writer).withSeparator(',').build();
        QueryAccess a = new QueryAccess() {

            @Override
            protected void processHeader(String[] line) {
                icsvWriter.writeNext(line);
            }

            @Override
            protected void processLine(String[] line) {
                icsvWriter.writeNext(line);
            }

        };
        a.call(queryRef);
        icsvWriter.flushQuietly();
    }

    /**
     * Get the response of a query as an ApiResponse object.
     *
     * @param queryRef the query reference
     * @return an ApiResponse object containing the response data
     * @throws FailedApiCallException         if the API call fails
     * @throws APINotReachableException       if the API is not reachable
     * @throws NotEnoughAPIInstancesException if there are not enough API instances available
     */
    public static ApiResponse get(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
        final ApiResponse response = new ApiResponse();
        QueryAccess a = new QueryAccess() {

            @Override
            protected void processHeader(String[] line) {
                response.setHeader(line);
            }

            @Override
            protected void processLine(String[] line) {
                response.add(line);
            }

        };
        a.call(queryRef);
        return response;
    }

}

1	package org.nanopub.extra.services;
2
3	import com.opencsv.CSVReader;
4	import com.opencsv.CSVWriterBuilder;
5	import com.opencsv.ICSVWriter;
6	import com.opencsv.exceptions.CsvValidationException;
7	import org.apache.http.HttpResponse;
8
9	import java.io.BufferedReader;
10	import java.io.IOException;
11	import java.io.InputStreamReader;
12	import java.io.Writer;
13
14	/**
15	* Second-generation query API access
16	*/
17	public abstract class QueryAccess {	3✔
18
19	/**
20	* Process the header.
21	*
22	* @param line the header line from the CSV response
23	*/
24	protected abstract void processHeader(String[] line);
25
26	/**
27	* Process a line of data from the CSV response.
28	*
29	* @param line the line of data from the CSV response
30	*/
31	protected abstract void processLine(String[] line);
32
33	/**
34	* Call a query with the given queryId and parameters.
35	*
36	* @param queryRef the query reference
37	* @throws FailedApiCallException if the API call fails
38	* @throws APINotReachableException if the API is not reachable
39	* @throws NotEnoughAPIInstancesException if there are not enough API instances available
40	*/
41	public void call(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
42	HttpResponse resp = QueryCall.run(queryRef);	3✔
43	try (CSVReader csvReader = new CSVReader(new BufferedReader(new InputStreamReader(resp.getEntity().getContent())))) {	13✔
44	String[] line = null;	2✔
45	int n = 0;	2✔
46	while ((line = csvReader.readNext()) != null) {	5✔
47	n++;	1✔
48	if (n == 1) {	3!
49	processHeader(line);	4✔
50	} else {
51	processLine(line);	×
52	}
53	}
54	} catch (IOException \| CsvValidationException ex) {	×
55	throw new FailedApiCallException(ex);	×
56	}	1✔
57	}	1✔
58
59	/**
60	* Print the response of a query in CSV format to the given writer.
61	*
62	* @param queryRef the query reference
63	* @param writer the writer to print the CSV response to
64	* @throws FailedApiCallException if the API call fails
65	* @throws APINotReachableException if the API is not reachable
66	* @throws NotEnoughAPIInstancesException if there are not enough API instances available
67	*/
68	public static void printCvsResponse(QueryRef queryRef, Writer writer) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
69	ICSVWriter icsvWriter = new CSVWriterBuilder(writer).withSeparator(',').build();	×
70	QueryAccess a = new QueryAccess() {	×
71
72	@Override
73	protected void processHeader(String[] line) {
74	icsvWriter.writeNext(line);	×
75	}	×
76
77	@Override
78	protected void processLine(String[] line) {
79	icsvWriter.writeNext(line);	×
80	}	×
81
82	};
83	a.call(queryRef);	×
84	icsvWriter.flushQuietly();	×
85	}	×
86
87	/**
88	* Get the response of a query as an ApiResponse object.
89	*
90	* @param queryRef the query reference
91	* @return an ApiResponse object containing the response data
92	* @throws FailedApiCallException if the API call fails
93	* @throws APINotReachableException if the API is not reachable
94	* @throws NotEnoughAPIInstancesException if there are not enough API instances available
95	*/
96	public static ApiResponse get(QueryRef queryRef) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
97	final ApiResponse response = new ApiResponse();	4✔
98	QueryAccess a = new QueryAccess() {	11✔
99
100	@Override
101	protected void processHeader(String[] line) {
102	response.setHeader(line);	4✔
103	}	1✔
104
105	@Override
106	protected void processLine(String[] line) {
107	response.add(line);	×
108	}	×
109
110	};
111	a.call(queryRef);	3✔
112	return response;	2✔
113	}
114
115	}

Nanopublication / nanopub-java / 19897067550

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