17376844338

Committed 01 Sep 2025 11:54AM UTC coverage: 45.468% (-0.03%) from 45.497%

Build # 17376844338

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: update code to use NanopubAlreadyFinalizedException

Run Details

825 of 2878 branches covered (28.67%)

Branch coverage included in aggregate %.

4608 of 9071 relevant lines covered (50.8%)

2.43 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

86.84

src/main/java/org/nanopub/fdo/RetrieveFdo.java

package org.nanopub.fdo;

import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.util.Values;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubAlreadyFinalizedException;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.extra.services.*;

import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.http.HttpClient;
import java.net.http.HttpRequest;
import java.net.http.HttpResponse;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Retrieve FDOs (FDO Records) from the nanopub network or handle system.
 */
// TODO class that provides the Op.Retrieve operations.
//      See https://fdo-connect.gitlab.io/ap1/architecture-documentation/main/operation-specification/
public class RetrieveFdo {

    /**
     * The query ID for retrieving FDOs by their ID from the nanopub network.
     */
    public final static String GET_FDO_QUERY_ID = "RAs0HI_KRAds4w_OOEMl-_ed0nZHFWdfePPXsDHf4kQkU/get-fdo-by-id";

    private RetrieveFdo() {
    }  // no instances allowed

    /**
     * Retrieve the NP/FdoRecord from the nanopub network or handle system, always check the nanopub network first.
     *
     * @param iriOrHandle the IRI or handle of the FDO to resolve
     * @return the FdoRecord corresponding to the IRI or handle
     * @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found in either the nanopub network or handle system
     */
    public static FdoRecord resolveId(String iriOrHandle) throws FdoNotFoundException {
        try {
            Nanopub np = resolveInNanopubNetwork(iriOrHandle);
            if (np != null) {
                return new FdoRecord(np);
            }
            if (FdoUtils.looksLikeHandle(iriOrHandle)) {
                return resolveInHandleSystem(iriOrHandle);
            } else if (FdoUtils.isHandleIri(Values.iri(iriOrHandle))) {
                return resolveInHandleSystem(FdoUtils.extractHandle(Values.iri(iriOrHandle)));
            }
        } catch (Exception e) {
            throw new FdoNotFoundException(e);
        }
        throw new FdoNotFoundException("Could not find fdo: " + iriOrHandle);
    }

    /**
     * Retrieve the newest corresponding Nanopub from the Nanopub network.
     *
     * @param iriOrHandle the IRI or handle of the FDO to resolve
     * @return the Nanopub corresponding to the IRI or handle, or null if not found
     * @throws org.nanopub.extra.services.FailedApiCallException if the API call fails
     */
    public static Nanopub resolveInNanopubNetwork(String iriOrHandle) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
        Map<String, String> params = new HashMap<>();
        params.put("fdoid", iriOrHandle);
        ApiResponse apiResponse = QueryAccess.get(GET_FDO_QUERY_ID, params);
        List<ApiResponseEntry> data = apiResponse.getData();
        if (data.isEmpty()) {
            return null;
        }
        String npRef = data.getFirst().get("np");
        return GetNanopub.get(npRef);
    }

    /**
     * Retrieve the data from the handle system.
     *
     * @param handle the handle of the FDO to resolve
     * @return the FdoRecord corresponding to the handle
     * @throws org.nanopub.MalformedNanopubException if the nanopub is malformed
     * @throws java.net.URISyntaxException           if the URI is malformed
     * @throws java.io.IOException                   if an I/O error occurs
     * @throws java.lang.InterruptedException        if the operation is interrupted
     */
    public static FdoRecord resolveInHandleSystem(String handle) throws MalformedNanopubException, URISyntaxException, IOException, InterruptedException, NanopubAlreadyFinalizedException {
        Nanopub np = FdoNanopubCreator.createFromHandleSystem(handle);
        return new FdoRecord(np);
    }

    /**
     * Retrieve the NP/FdoRecord Content (DataRef) from the nanopub network or handle system, always check the nanopub network first.
     *
     * @param iriOrHandle the IRI or handle of the FDO to resolve
     * @return an InputStream containing the content of the FDO
     * @throws java.net.URISyntaxException          if the URI is malformed
     * @throws java.io.IOException                  if an I/O error occurs
     * @throws java.lang.InterruptedException       if the operation is interrupted
     * @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found
     */
    public static InputStream retrieveContentFromId(String iriOrHandle) throws URISyntaxException, IOException, InterruptedException, FdoNotFoundException {
        FdoRecord fdo = resolveId(iriOrHandle);

        Value contentUrl = fdo.getDataRef();
        if (contentUrl == null) {
            throw new FdoNotFoundException("FDO has no file / DataRef.");
        }
        HttpRequest req = HttpRequest.newBuilder().GET().uri(new URI(contentUrl.stringValue())).build();
        HttpResponse<InputStream> httpResponse = HttpClient.newHttpClient().send(req, responseInfo -> HttpResponse.BodySubscribers.ofInputStream());
        return httpResponse.body();
    }

}

1	package org.nanopub.fdo;
2
3	import org.eclipse.rdf4j.model.Value;
4	import org.eclipse.rdf4j.model.util.Values;
5	import org.nanopub.MalformedNanopubException;
6	import org.nanopub.Nanopub;
7	import org.nanopub.NanopubAlreadyFinalizedException;
8	import org.nanopub.extra.server.GetNanopub;
9	import org.nanopub.extra.services.*;
10
11	import java.io.IOException;
12	import java.io.InputStream;
13	import java.net.URI;
14	import java.net.URISyntaxException;
15	import java.net.http.HttpClient;
16	import java.net.http.HttpRequest;
17	import java.net.http.HttpResponse;
18	import java.util.HashMap;
19	import java.util.List;
20	import java.util.Map;
21
22	/**
23	* Retrieve FDOs (FDO Records) from the nanopub network or handle system.
24	*/
25	// TODO class that provides the Op.Retrieve operations.
26	// See https://fdo-connect.gitlab.io/ap1/architecture-documentation/main/operation-specification/
27	public class RetrieveFdo {
28
29	/**
30	* The query ID for retrieving FDOs by their ID from the nanopub network.
31	*/
32	public final static String GET_FDO_QUERY_ID = "RAs0HI_KRAds4w_OOEMl-_ed0nZHFWdfePPXsDHf4kQkU/get-fdo-by-id";
33
34	private RetrieveFdo() {
35	} // no instances allowed
36
37	/**
38	* Retrieve the NP/FdoRecord from the nanopub network or handle system, always check the nanopub network first.
39	*
40	* @param iriOrHandle the IRI or handle of the FDO to resolve
41	* @return the FdoRecord corresponding to the IRI or handle
42	* @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found in either the nanopub network or handle system
43	*/
44	public static FdoRecord resolveId(String iriOrHandle) throws FdoNotFoundException {
45	try {
46	Nanopub np = resolveInNanopubNetwork(iriOrHandle);	3✔
47	if (np != null) {	2✔
48	return new FdoRecord(np);	5✔
49	}
50	if (FdoUtils.looksLikeHandle(iriOrHandle)) {	3✔
51	return resolveInHandleSystem(iriOrHandle);	3✔
52	} else if (FdoUtils.isHandleIri(Values.iri(iriOrHandle))) {	4!
53	return resolveInHandleSystem(FdoUtils.extractHandle(Values.iri(iriOrHandle)));	5✔
54	}
55	} catch (Exception e) {	1✔
56	throw new FdoNotFoundException(e);	5✔
57	}	×
58	throw new FdoNotFoundException("Could not find fdo: " + iriOrHandle);	×
59	}
60
61	/**
62	* Retrieve the newest corresponding Nanopub from the Nanopub network.
63	*
64	* @param iriOrHandle the IRI or handle of the FDO to resolve
65	* @return the Nanopub corresponding to the IRI or handle, or null if not found
66	* @throws org.nanopub.extra.services.FailedApiCallException if the API call fails
67	*/
68	public static Nanopub resolveInNanopubNetwork(String iriOrHandle) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
69	Map<String, String> params = new HashMap<>();	4✔
70	params.put("fdoid", iriOrHandle);	5✔
71	ApiResponse apiResponse = QueryAccess.get(GET_FDO_QUERY_ID, params);	4✔
72	List<ApiResponseEntry> data = apiResponse.getData();	3✔
73	if (data.isEmpty()) {	3✔
74	return null;	2✔
75	}
76	String npRef = data.getFirst().get("np");	6✔
77	return GetNanopub.get(npRef);	3✔
78	}
79
80	/**
81	* Retrieve the data from the handle system.
82	*
83	* @param handle the handle of the FDO to resolve
84	* @return the FdoRecord corresponding to the handle
85	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed
86	* @throws java.net.URISyntaxException if the URI is malformed
87	* @throws java.io.IOException if an I/O error occurs
88	* @throws java.lang.InterruptedException if the operation is interrupted
89	*/
90	public static FdoRecord resolveInHandleSystem(String handle) throws MalformedNanopubException, URISyntaxException, IOException, InterruptedException, NanopubAlreadyFinalizedException {
91	Nanopub np = FdoNanopubCreator.createFromHandleSystem(handle);	3✔
92	return new FdoRecord(np);	5✔
93	}
94
95	/**
96	* Retrieve the NP/FdoRecord Content (DataRef) from the nanopub network or handle system, always check the nanopub network first.
97	*
98	* @param iriOrHandle the IRI or handle of the FDO to resolve
99	* @return an InputStream containing the content of the FDO
100	* @throws java.net.URISyntaxException if the URI is malformed
101	* @throws java.io.IOException if an I/O error occurs
102	* @throws java.lang.InterruptedException if the operation is interrupted
103	* @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found
104	*/
105	public static InputStream retrieveContentFromId(String iriOrHandle) throws URISyntaxException, IOException, InterruptedException, FdoNotFoundException {
106	FdoRecord fdo = resolveId(iriOrHandle);	3✔
107
108	Value contentUrl = fdo.getDataRef();	3✔
109	if (contentUrl == null) {	2!
110	throw new FdoNotFoundException("FDO has no file / DataRef.");	×
111	}
112	HttpRequest req = HttpRequest.newBuilder().GET().uri(new URI(contentUrl.stringValue())).build();	10✔
113	HttpResponse<InputStream> httpResponse = HttpClient.newHttpClient().send(req, responseInfo -> HttpResponse.BodySubscribers.ofInputStream());	5✔
114	return httpResponse.body();	4✔
115	}
116
117	}

Nanopublication / nanopub-java / 17376844338

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous