17852246692

Committed 19 Sep 2025 07:56AM UTC coverage: 51.799% (+0.9%) from 50.885%

Build # 17852246692

Build Type

push

github

Committed by

tkuhn

Commit Message

feat: Add QueryRef and use multimap

- Simplifies usage of query references
- Allows for multi-values per key for new queries with multi-placeholder

Run Details

996 of 2882 branches covered (34.56%)

Branch coverage included in aggregate %.

5166 of 9014 relevant lines covered (57.31%)

2.69 hits per line

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86.11

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

package org.nanopub.fdo;

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.List;

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.APINotReachableException;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.FailedApiCallException;
import org.nanopub.extra.services.NotEnoughAPIInstancesException;
import org.nanopub.extra.services.QueryAccess;
import org.nanopub.extra.services.QueryRef;

/**
 * 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 {
        ApiResponse apiResponse = QueryAccess.get(new QueryRef(GET_FDO_QUERY_ID, "fdoid", iriOrHandle));
        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 java.io.IOException;
4	import java.io.InputStream;
5	import java.net.URI;
6	import java.net.URISyntaxException;
7	import java.net.http.HttpClient;
8	import java.net.http.HttpRequest;
9	import java.net.http.HttpResponse;
10	import java.util.List;
11
12	import org.eclipse.rdf4j.model.Value;
13	import org.eclipse.rdf4j.model.util.Values;
14	import org.nanopub.MalformedNanopubException;
15	import org.nanopub.Nanopub;
16	import org.nanopub.NanopubAlreadyFinalizedException;
17	import org.nanopub.extra.server.GetNanopub;
18	import org.nanopub.extra.services.APINotReachableException;
19	import org.nanopub.extra.services.ApiResponse;
20	import org.nanopub.extra.services.ApiResponseEntry;
21	import org.nanopub.extra.services.FailedApiCallException;
22	import org.nanopub.extra.services.NotEnoughAPIInstancesException;
23	import org.nanopub.extra.services.QueryAccess;
24	import org.nanopub.extra.services.QueryRef;
25
26	/**
27	* Retrieve FDOs (FDO Records) from the nanopub network or handle system.
28	*/
29	// TODO class that provides the Op.Retrieve operations.
30	// See https://fdo-connect.gitlab.io/ap1/architecture-documentation/main/operation-specification/
31	public class RetrieveFdo {
32
33	/**
34	* The query ID for retrieving FDOs by their ID from the nanopub network.
35	*/
36	public final static String GET_FDO_QUERY_ID = "RAs0HI_KRAds4w_OOEMl-_ed0nZHFWdfePPXsDHf4kQkU/get-fdo-by-id";
37
38	private RetrieveFdo() {
39	} // no instances allowed
40
41	/**
42	* Retrieve the NP/FdoRecord from the nanopub network or handle system, always check the nanopub network first.
43	*
44	* @param iriOrHandle the IRI or handle of the FDO to resolve
45	* @return the FdoRecord corresponding to the IRI or handle
46	* @throws org.nanopub.fdo.FdoNotFoundException if the FDO is not found in either the nanopub network or handle system
47	*/
48	public static FdoRecord resolveId(String iriOrHandle) throws FdoNotFoundException {
49	try {
50	Nanopub np = resolveInNanopubNetwork(iriOrHandle);	3✔
51	if (np != null) {	2✔
52	return new FdoRecord(np);	5✔
53	}
54	if (FdoUtils.looksLikeHandle(iriOrHandle)) {	3✔
55	return resolveInHandleSystem(iriOrHandle);	3✔
56	} else if (FdoUtils.isHandleIri(Values.iri(iriOrHandle))) {	4!
57	return resolveInHandleSystem(FdoUtils.extractHandle(Values.iri(iriOrHandle)));	5✔
58	}
59	} catch (Exception e) {	1✔
60	throw new FdoNotFoundException(e);	5✔
61	}	×
62	throw new FdoNotFoundException("Could not find fdo: " + iriOrHandle);	×
63	}
64
65	/**
66	* Retrieve the newest corresponding Nanopub from the Nanopub network.
67	*
68	* @param iriOrHandle the IRI or handle of the FDO to resolve
69	* @return the Nanopub corresponding to the IRI or handle, or null if not found
70	* @throws org.nanopub.extra.services.FailedApiCallException if the API call fails
71	*/
72	public static Nanopub resolveInNanopubNetwork(String iriOrHandle) throws FailedApiCallException, APINotReachableException, NotEnoughAPIInstancesException {
73	ApiResponse apiResponse = QueryAccess.get(new QueryRef(GET_FDO_QUERY_ID, "fdoid", iriOrHandle));	8✔
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, NanopubAlreadyFinalizedException {
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 / 17852246692

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