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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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.extra.server.GetNanopub;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.FailedApiCallException;
import org.nanopub.extra.services.QueryAccess;

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 {
        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 {
        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.extra.server.GetNanopub;
8	import org.nanopub.extra.services.ApiResponse;
9	import org.nanopub.extra.services.ApiResponseEntry;
10	import org.nanopub.extra.services.FailedApiCallException;
11	import org.nanopub.extra.services.QueryAccess;
12
13	import java.io.IOException;
14	import java.io.InputStream;
15	import java.net.URI;
16	import java.net.URISyntaxException;
17	import java.net.http.HttpClient;
18	import java.net.http.HttpRequest;
19	import java.net.http.HttpResponse;
20	import java.util.HashMap;
21	import java.util.List;
22	import java.util.Map;
23
24	/**
25	* Retrieve FDOs (FDO Records) from the nanopub network or handle system.
26	*/
27	// TODO class that provides the Op.Retrieve operations.
28	// See https://fdo-connect.gitlab.io/ap1/architecture-documentation/main/operation-specification/
29	public class RetrieveFdo {
30
31	/**
32	* The query ID for retrieving FDOs by their ID from the nanopub network.
33	*/
34	public final static String GET_FDO_QUERY_ID = "RAs0HI_KRAds4w_OOEMl-_ed0nZHFWdfePPXsDHf4kQkU/get-fdo-by-id";
35
36	private RetrieveFdo() {
37	} // no instances allowed
38
39	/**
40	* Retrieve the NP/FdoRecord from the nanopub network or handle system, always check the nanopub network first.
41	*
42	* @param iriOrHandle the IRI or handle of the FDO to resolve
43	* @return the FdoRecord corresponding to the IRI or handle
44	* @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found in either the nanopub network or handle system
45	*/
46	public static FdoRecord resolveId(String iriOrHandle) throws FdoNotFoundException {
47	try {
48	Nanopub np = resolveInNanopubNetwork(iriOrHandle);	3✔
49	if (np != null) {	2✔
50	return new FdoRecord(np);	5✔
51	}
52	if (FdoUtils.looksLikeHandle(iriOrHandle)) {	3✔
53	return resolveInHandleSystem(iriOrHandle);	3✔
54	} else if (FdoUtils.isHandleIri(Values.iri(iriOrHandle))) {	4!
55	return resolveInHandleSystem(FdoUtils.extractHandle(Values.iri(iriOrHandle)));	5✔
56	}
57	} catch (Exception e) {	1✔
58	throw new FdoNotFoundException(e);	5✔
59	}	×
60	throw new FdoNotFoundException("Could not find fdo: " + iriOrHandle);	×
61	}
62
63	/**
64	* Retrieve the newest corresponding Nanopub from the Nanopub network.
65	*
66	* @param iriOrHandle the IRI or handle of the FDO to resolve
67	* @return the Nanopub corresponding to the IRI or handle, or null if not found
68	* @throws org.nanopub.extra.services.FailedApiCallException if the API call fails
69	*/
70	public static Nanopub resolveInNanopubNetwork(String iriOrHandle) throws FailedApiCallException {
71	Map<String, String> params = new HashMap<>();	4✔
72	params.put("fdoid", iriOrHandle);	5✔
73	ApiResponse apiResponse = QueryAccess.get(GET_FDO_QUERY_ID, params);	4✔
74	List<ApiResponseEntry> data = apiResponse.getData();	3✔
75	if (data.isEmpty()) {	3✔
76	return null;	2✔
77	}
78	String npRef = data.getFirst().get("np");	6✔
79	return GetNanopub.get(npRef);	3✔
80	}
81
82	/**
83	* Retrieve the data from the handle system.
84	*
85	* @param handle the handle of the FDO to resolve
86	* @return the FdoRecord corresponding to the handle
87	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed
88	* @throws java.net.URISyntaxException if the URI is malformed
89	* @throws java.io.IOException if an I/O error occurs
90	* @throws java.lang.InterruptedException if the operation is interrupted
91	*/
92	public static FdoRecord resolveInHandleSystem(String handle) throws MalformedNanopubException, URISyntaxException, IOException, InterruptedException {
93	Nanopub np = FdoNanopubCreator.createFromHandleSystem(handle);	3✔
94	return new FdoRecord(np);	5✔
95	}
96
97	/**
98	* Retrieve the NP/FdoRecord Content (DataRef) from the nanopub network or handle system, always check the nanopub network first.
99	*
100	* @param iriOrHandle the IRI or handle of the FDO to resolve
101	* @return an InputStream containing the content of the FDO
102	* @throws java.net.URISyntaxException if the URI is malformed
103	* @throws java.io.IOException if an I/O error occurs
104	* @throws java.lang.InterruptedException if the operation is interrupted
105	* @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found
106	*/
107	public static InputStream retrieveContentFromId(String iriOrHandle) throws URISyntaxException, IOException, InterruptedException, FdoNotFoundException {
108	FdoRecord fdo = resolveId(iriOrHandle);	3✔
109
110	Value contentUrl = fdo.getDataRef();	3✔
111	if (contentUrl == null) {	2!
112	throw new FdoNotFoundException("FDO has no file / DataRef.");	×
113	}
114	HttpRequest req = HttpRequest.newBuilder().GET().uri(new URI(contentUrl.stringValue())).build();	10✔
115	HttpResponse<InputStream> httpResponse = HttpClient.newHttpClient().send(req, responseInfo -> HttpResponse.BodySubscribers.ofInputStream());	5✔
116	return httpResponse.body();	4✔
117	}
118
119	}

Nanopublication / nanopub-java / 17069388833

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