24565015084

Committed 17 Apr 2026 12:27PM UTC coverage: 17.442% (+1.6%) from 15.798%

Build # 24565015084

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web-flow

Commit Message

Merge pull request #441 from knowledgepixels/refactoring-LookupApis

Refactoring lookup apis

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src/main/java/com/knowledgepixels/nanodash/LookupApis.java

package com.knowledgepixels.nanodash;

import java.io.InputStream;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.Map;

import org.apache.commons.io.IOUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.HttpResponse;
import org.apache.http.NameValuePair;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.utils.URLEncodedUtils;
import org.apache.http.util.EntityUtils;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.QueryRef;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.beust.jcommander.Strings;
import com.github.openjson.JSONArray;
import com.github.openjson.JSONObject;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import com.knowledgepixels.nanodash.component.QueryParamField;

/**
 * Utility class for APIs look up and parsing.
 */
public class LookupApis {

    private static final Logger logger = LoggerFactory.getLogger(LookupApis.class);

    private LookupApis() {
    }  // no instances allowed

    /**
     * Parses a JSON response from a grlc API for nanopublications and extracts URIs and labels.
     *
     * @param grlcJsonObject the JSON object containing the grlc API response
     * @param labelMap       a map to store URIs and their corresponding labels
     * @param values         a list to store the extracted URIs
     */
    public static void parseNanopubGrlcApi(JSONObject grlcJsonObject, Map<String, String> labelMap, List<String> values) {
        // Aimed to resolve Nanopub grlc API: http://grlc.nanopubs.lod.labs.vu.nl/api/local/local/find_signed_nanopubs_with_text?text=covid
        JSONArray resultsArray = grlcJsonObject.getJSONObject("results").getJSONArray("bindings");
        for (int i = 0; i < resultsArray.length(); i++) {
            JSONObject resultObject = resultsArray.getJSONObject(i);
            // Get the nanopub URI
            String uri = resultObject.getJSONObject("thing").getString("value");
            // Get the string which matched with the search term
            String label = resultObject.getJSONObject("label").getString("value");
            values.add(uri);
            labelMap.put(uri, label);
        }
    }

    /**
     * Fetches possible values from an API based on the provided search term.
     *
     * @param apiString  the API endpoint URL to query
     * @param searchterm the search term to use for querying the API
     * @param labelMap   a map to store URIs and their corresponding labels
     * @param values     a list to store the extracted URIs
     */
    public static void getPossibleValues(String apiString, String searchterm, Map<String, String> labelMap, List<String> values) {
        // TODO This method is a mess and needs some serious clean-up and structuring...
        try {
            if (apiString.startsWith("https://w3id.org/np/l/nanopub-query-1.1/api/") || apiString.startsWith("http://purl.org/nanopub/api/find_signed_things?")) {
                lookupNanopubNetwork(apiString, searchterm, labelMap, values);
                return;
            }

            if (apiString.startsWith("https://vodex.")) {
                searchterm = expandSearchTerm(searchterm);
            }
            String callUrl;
            if (apiString.contains(" ")) {
                callUrl = apiString.replaceAll(" ", URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString()));
            } else {
                callUrl = apiString + URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString());
            }
            HttpGet get = new HttpGet(callUrl);
            get.setHeader(HttpHeaders.ACCEPT, "application/json");
            get.setHeader("User-Agent", NanodashPreferences.get().getWebsiteUrl() + "#user-agent");
            String respString;
            try (CloseableHttpClient client = HttpClientBuilder.create().build()) {
                HttpResponse resp = client.execute(get);
                if (resp.getStatusLine().getStatusCode() == 405) {
                    // Method not allowed, trying POST
                    EntityUtils.consume(resp.getEntity());
                    HttpPost post = new HttpPost(apiString + URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString()));
                    resp = client.execute(post);
                }
                // TODO: support other content types (CSV, XML, ...)
                // System.err.println(resp.getHeaders("Content-Type")[0]);
                try (InputStream in = resp.getEntity().getContent()) {
                    respString = IOUtils.toString(in, StandardCharsets.UTF_8);
                }
            }
            // System.out.println(respString);

            if (apiString.startsWith("https://w3id.org/np/l/nanopub-query") || apiString.startsWith("https://grlc.") || apiString.contains("/sparql?")) {
                parseNanopubGrlcApi(new JSONObject(respString), labelMap, values);
            } else if (apiString.startsWith("https://www.ebi.ac.uk/ols/api/select")) {
                // Resolve EBI Ontology Lookup Service
                // e.g. https://www.ebi.ac.uk/ols/api/select?q=interacts%20with
                // response.docs.[].iri/label
                JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");
                for (int i = 0; i < responseArray.length(); i++) {
                    String uri = responseArray.getJSONObject(i).getString("iri");
                    String label = responseArray.getJSONObject(i).getString("label");
                    try {
                        label += " - " + responseArray.getJSONObject(i).getJSONArray("description").getString(0);
                    } catch (Exception ex) {
                        logger.error("No description found for {}", uri, ex);
                    }
                    if (!values.contains(uri)) {
                        values.add(uri);
                        labelMap.put(uri, label);
                    }
                }
            } else if (apiString.startsWith("https://api.openaire.eu/graph/v")) {
                String type = apiString.replaceFirst("^https://api\\.openaire\\.eu/graph/(v[0-9]+/[a-zA-Z]+).*$", "$1");
                for (Object obj : new JSONObject(respString).getJSONArray("results")) {
                    if (obj instanceof JSONObject jsonObj) {
                        String uri = "https://api.openaire.eu/graph/" + type + "/" + jsonObj.getString("id");
                        if (!values.contains(uri)) {
                            values.add(uri);
                            String label = uri;
                            if (jsonObj.has("mainTitle")) {
                                label = jsonObj.getString("mainTitle");
                            } else if (jsonObj.has("legalShortName")) {
                                label = jsonObj.getString("legalShortName");
                            } else if (jsonObj.has("officialName")) {
                                label = jsonObj.getString("officialName");
                            } else if (jsonObj.has("title")) {
                                label = jsonObj.getString("title");
                            } else if (jsonObj.has("familyName")) {
                                label = jsonObj.getString("familyName");
                                if (jsonObj.has("givenName")) {
                                    label = jsonObj.getString("givenName") + " " + label;
                                }
                            }
                            labelMap.put(uri, label);
                        }
                    }
                }
            } else if (apiString.startsWith("https://api.gbif.org/v1/species/suggest")) {
                JSONArray responseArray = new JSONArray(respString);
                for (int i = 0; i < responseArray.length(); i++) {
                    String uri = "https://www.gbif.org/species/" + responseArray.getJSONObject(i).getString("key");
                    String label = responseArray.getJSONObject(i).getString("scientificName");
                    if (!values.contains(uri)) {
                        values.add(uri);
                        labelMap.put(uri, label);
                    }
                }
            } else if (apiString.startsWith("https://api.catalogueoflife.org/dataset/3LR/nameusage/search")) {
                JSONArray responseArray = new JSONObject(respString).getJSONArray("result");
                for (int i = 0; i < responseArray.length(); i++) {
                    String uri = "https://www.catalogueoflife.org/data/taxon/" + responseArray.getJSONObject(i).getString("id");
                    String label = responseArray.getJSONObject(i).getJSONObject("usage").getString("label");
                    if (!values.contains(uri)) {
                        values.add(uri);
                        labelMap.put(uri, label);
                    }
                }
            } else if (apiString.startsWith("https://vodex.")) {
                // TODO This is just a test and needs to be improved
                JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");
                for (int i = 0; i < responseArray.length(); i++) {
                    String uri = responseArray.getJSONObject(i).getString("id");
                    String label = responseArray.getJSONObject(i).getJSONArray("label").get(0).toString();
                    if (!values.contains(uri)) {
                        values.add(uri);
                        labelMap.put(uri, label);
                    }
                }
            } else if (apiString.startsWith("https://api.ror.org/organizations")) {
                // TODO This is just a test and needs to be improved
                JSONArray responseArray = new JSONObject(respString).getJSONArray("items");
                for (int i = 0; i < responseArray.length(); i++) {
                    String uri = responseArray.getJSONObject(i).getString("id");
                    JSONArray namesArray = responseArray.getJSONObject(i).getJSONArray("names");
                    if (namesArray.length() == 0) continue;
                    String label = namesArray.getJSONObject(0).getString("value");
                    if (!values.contains(uri)) {
                        values.add(uri);
                        labelMap.put(uri, label);
                    }
                }
            } else {
                // TODO: create parseJsonApi() ?
                boolean foundId = false;
                JSONObject json = new JSONObject(respString);
                for (String key : json.keySet()) {
                    if (values.size() > 9) break;
                    if (!(json.get(key) instanceof JSONArray)) continue;
                    JSONArray a = json.getJSONArray(key);
                    for (int i = 0; i < a.length(); i++) {
                        if (values.size() > 9) break;
                        if (!(a.get(i) instanceof JSONObject)) continue;
                        JSONObject o = a.getJSONObject(i);
                        String uri = null;
                        for (String s : new String[]{"@id", "concepturi", "uri"}) {
                            if (o.has(s)) {
                                uri = o.get(s).toString();
                                foundId = true;
                                break;
                            }
                        }
                        if (uri != null) {
                            values.add(uri);
                            String label = "";
                            for (String s : new String[]{"prefLabel", "label"}) {
                                if (o.has(s)) {
                                    label = o.get(s).toString().replaceAll(" - ", " -- ");
                                    break;
                                }
                            }
                            String desc = "";
                            for (String s : new String[]{"definition", "description"}) {
                                if (o.has(s)) {
                                    desc = o.get(s).toString();
                                    break;
                                }
                            }
                            if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;
                            labelMap.put(uri, label + desc);
                        }
                    }
                }
                if (foundId == false) {
                    // ID key not found, try to get results for following format
                    // {result1: ["label 1", "label 2"], result2: ["label 3", "label 4"]}
                    // Aims to resolve https://name-resolution-sri.renci.org/docs#

                    // TODO: It seems this is triggered too often and adds 'https://identifiers.org/search' when it
                    //       shouldn't. Manually filtering these out for now...
                    for (String key : json.keySet()) {
                        if (!(json.get(key) instanceof JSONArray)) continue;
                        if ("search".equals(key)) continue;
                        JSONArray labelArray = json.getJSONArray(key);
                        String uri = key;
                        String label = "";
                        String desc = "";
                        if (labelArray.length() > 0) label = labelArray.getString(0);
                        if (labelArray.length() > 1) desc = labelArray.getString(1);
                        if (desc.length() > 80) desc = desc.substring(0, 77) + "...";
                        if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;
                        // Quick fix to convert CURIE to URI, as Nanodash only accepts URIs here
                        if (!(uri.startsWith("http://") || uri.startsWith("https://"))) {
                            uri = "https://identifiers.org/" + uri;
                        }
                        values.add(uri);
                        labelMap.put(uri, label + desc);
                    }
                }
            }
        } catch (Exception ex) {
            logger.error("Error fetching possible values from API: {}", apiString, ex);
        }
    }

    private static void lookupNanopubNetwork(String apiString, String searchterm, Map<String, String> labelMap, List<String> values) {
        String queryId = QueryApiAccess.FIND_THINGS;
        if (apiString.startsWith("https://w3id.org/np/l/nanopub-query-1.1/api/")) {
            queryId = apiString.replace("https://w3id.org/np/l/nanopub-query-1.1/api/", "");
            if (queryId.contains("?")) queryId = queryId.substring(0, queryId.indexOf("?"));
        }
        Multimap<String, String> params = ArrayListMultimap.create();
        if (apiString.contains("?")) {
            List<NameValuePair> urlParams = URLEncodedUtils.parse(apiString.substring(apiString.indexOf("?") + 1), StandardCharsets.UTF_8);
            for (NameValuePair p : urlParams) {
                params.put(p.getName(), p.getValue());
            }
        }
        GrlcQuery q = GrlcQuery.get(queryId);
        if (q.getEndpoint().stringValue().endsWith("/text")) {
            searchterm = expandSearchTerm(searchterm);
        }
        String queryParamName = "query";
        if (q.getPlaceholdersList().size() == 1) {
            queryParamName = QueryParamField.getParamName(q.getPlaceholdersList().get(0));
        }
        params.put(queryParamName, searchterm);
        ApiResponse result = ApiCache.retrieveResponseSync(new QueryRef(queryId, params), false);
        int count = 0;
        for (ApiResponseEntry r : result.getData()) {
            String uri = r.get("thing");
            values.add(uri);
            String desc = r.get("description");
            if (desc == null) desc = "";
            if (desc.length() > 80) desc = desc.substring(0, 77) + "...";
            if (!desc.isEmpty()) desc = " - " + desc;
            labelMap.put(uri, r.get("label") + desc);
            count++;
            if (count > 9) return;
        }
    }

    private static String expandSearchTerm(String searchTerm) {
        String expanded = "";
        boolean insideQuotes = false;
        searchTerm = searchTerm.replaceAll("\\s+", " ").trim();
        for (char c : searchTerm.toCharArray()) {
            if (c == '\n') {
                continue;
            } else if (c == '"') {
                expanded += '"';
                insideQuotes = !insideQuotes;
            } else if (c == ' ') {
                if (insideQuotes) {
                    expanded += ' ';
                } else {
                    expanded += '\n';
                }
            } else if (("" + c).matches("\\w") || c == '-' || c == '_') {
                expanded += c;
            } else {
                if (insideQuotes) {
                    expanded += ' ';
                } else {
                    expanded += '\n';
                }
            }
        }
        String extra = "*";
        expanded = expanded.replaceAll("\\n+", "\n").replaceAll("\"", "\\\\\\\"").trim();
        if (expanded.endsWith("\"") || insideQuotes) extra = "";
        return "( " + Strings.join(" AND ", expanded.split("\n")) + extra + " )";
    }

}

1	package com.knowledgepixels.nanodash;
2
3	import java.io.InputStream;
4	import java.net.URLEncoder;
5	import java.nio.charset.StandardCharsets;
6	import java.util.List;
7	import java.util.Map;
8
9	import org.apache.commons.io.IOUtils;
10	import org.apache.http.HttpHeaders;
11	import org.apache.http.HttpResponse;
12	import org.apache.http.NameValuePair;
13	import org.apache.http.client.methods.HttpGet;
14	import org.apache.http.client.methods.HttpPost;
15	import org.apache.http.client.utils.URLEncodedUtils;
16	import org.apache.http.util.EntityUtils;
17	import org.apache.http.impl.client.CloseableHttpClient;
18	import org.apache.http.impl.client.HttpClientBuilder;
19	import org.nanopub.extra.services.ApiResponse;
20	import org.nanopub.extra.services.ApiResponseEntry;
21	import org.nanopub.extra.services.QueryRef;
22	import org.slf4j.Logger;
23	import org.slf4j.LoggerFactory;
24
25	import com.beust.jcommander.Strings;
26	import com.github.openjson.JSONArray;
27	import com.github.openjson.JSONObject;
28	import com.google.common.collect.ArrayListMultimap;
29	import com.google.common.collect.Multimap;
30	import com.knowledgepixels.nanodash.component.QueryParamField;
31
32	/**
33	* Utility class for APIs look up and parsing.
34	*/
35	public class LookupApis {
36
37	private static final Logger logger = LoggerFactory.getLogger(LookupApis.class);	12✔
38
39	private LookupApis() {
40	} // no instances allowed
41
42	/**
43	* Parses a JSON response from a grlc API for nanopublications and extracts URIs and labels.
44	*
45	* @param grlcJsonObject the JSON object containing the grlc API response
46	* @param labelMap a map to store URIs and their corresponding labels
47	* @param values a list to store the extracted URIs
48	*/
49	public static void parseNanopubGrlcApi(JSONObject grlcJsonObject, Map<String, String> labelMap, List<String> values) {
50	// Aimed to resolve Nanopub grlc API: http://grlc.nanopubs.lod.labs.vu.nl/api/local/local/find_signed_nanopubs_with_text?text=covid
51	JSONArray resultsArray = grlcJsonObject.getJSONObject("results").getJSONArray("bindings");	18✔
52	for (int i = 0; i < resultsArray.length(); i++) {	24✔
53	JSONObject resultObject = resultsArray.getJSONObject(i);	12✔
54	// Get the nanopub URI
55	String uri = resultObject.getJSONObject("thing").getString("value");	18✔
56	// Get the string which matched with the search term
57	String label = resultObject.getJSONObject("label").getString("value");	18✔
58	values.add(uri);	12✔
59	labelMap.put(uri, label);	15✔
60	}
61	}	3✔
62
63	/**
64	* Fetches possible values from an API based on the provided search term.
65	*
66	* @param apiString the API endpoint URL to query
67	* @param searchterm the search term to use for querying the API
68	* @param labelMap a map to store URIs and their corresponding labels
69	* @param values a list to store the extracted URIs
70	*/
71	public static void getPossibleValues(String apiString, String searchterm, Map<String, String> labelMap, List<String> values) {
72	// TODO This method is a mess and needs some serious clean-up and structuring...
73	try {
74	if (apiString.startsWith("https://w3id.org/np/l/nanopub-query-1.1/api/") \|\| apiString.startsWith("http://purl.org/nanopub/api/find_signed_things?")) {	24✔
75	lookupNanopubNetwork(apiString, searchterm, labelMap, values);	15✔
76	return;	3✔
77	}
78
79	if (apiString.startsWith("https://vodex.")) {	12✔
80	searchterm = expandSearchTerm(searchterm);	9✔
81	}
82	String callUrl;
83	if (apiString.contains(" ")) {	12✔
84	callUrl = apiString.replaceAll(" ", URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString()));	27✔
85	} else {
86	callUrl = apiString + URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString());	21✔
87	}
88	HttpGet get = new HttpGet(callUrl);	15✔
89	get.setHeader(HttpHeaders.ACCEPT, "application/json");	12✔
90	get.setHeader("User-Agent", NanodashPreferences.get().getWebsiteUrl() + "#user-agent");	18✔
91	String respString;
92	try (CloseableHttpClient client = HttpClientBuilder.create().build()) {	9✔
93	HttpResponse resp = client.execute(get);	12✔
94	if (resp.getStatusLine().getStatusCode() == 405) {	15!
95	// Method not allowed, trying POST
96	EntityUtils.consume(resp.getEntity());	×
97	HttpPost post = new HttpPost(apiString + URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString()));	×
98	resp = client.execute(post);	×
99	}
100	// TODO: support other content types (CSV, XML, ...)
101	// System.err.println(resp.getHeaders("Content-Type")[0]);
102	try (InputStream in = resp.getEntity().getContent()) {	12✔
103	respString = IOUtils.toString(in, StandardCharsets.UTF_8);	12✔
104	}
105	}
106	// System.out.println(respString);
107
108	if (apiString.startsWith("https://w3id.org/np/l/nanopub-query") \|\| apiString.startsWith("https://grlc.") \|\| apiString.contains("/sparql?")) {	36✔
109	parseNanopubGrlcApi(new JSONObject(respString), labelMap, values);	24✔
110	} else if (apiString.startsWith("https://www.ebi.ac.uk/ols/api/select")) {	12✔
111	// Resolve EBI Ontology Lookup Service
112	// e.g. https://www.ebi.ac.uk/ols/api/select?q=interacts%20with
113	// response.docs.[].iri/label
114	JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");	27✔
115	for (int i = 0; i < responseArray.length(); i++) {	24✔
116	String uri = responseArray.getJSONObject(i).getString("iri");	18✔
117	String label = responseArray.getJSONObject(i).getString("label");	18✔
118	try {
119	label += " - " + responseArray.getJSONObject(i).getJSONArray("description").getString(0);	30✔
120	} catch (Exception ex) {	×
121	logger.error("No description found for {}", uri, ex);	×
122	}	3✔
123	if (!values.contains(uri)) {	12!
124	values.add(uri);	12✔
125	labelMap.put(uri, label);	15✔
126	}
127	}
128	} else if (apiString.startsWith("https://api.openaire.eu/graph/v")) {	15✔
129	String type = apiString.replaceFirst("^https://api\\.openaire\\.eu/graph/(v[0-9]+/[a-zA-Z]+).*$", "$1");	15✔
130	for (Object obj : new JSONObject(respString).getJSONArray("results")) {	42✔
131	if (obj instanceof JSONObject jsonObj) {	18!
132	String uri = "https://api.openaire.eu/graph/" + type + "/" + jsonObj.getString("id");	18✔
133	if (!values.contains(uri)) {	12!
134	values.add(uri);	12✔
135	String label = uri;	6✔
136	if (jsonObj.has("mainTitle")) {	12!
137	label = jsonObj.getString("mainTitle");	15✔
138	} else if (jsonObj.has("legalShortName")) {	×
139	label = jsonObj.getString("legalShortName");	×
140	} else if (jsonObj.has("officialName")) {	×
141	label = jsonObj.getString("officialName");	×
142	} else if (jsonObj.has("title")) {	×
143	label = jsonObj.getString("title");	×
144	} else if (jsonObj.has("familyName")) {	×
145	label = jsonObj.getString("familyName");	×
146	if (jsonObj.has("givenName")) {	×
147	label = jsonObj.getString("givenName") + " " + label;	×
148	}
149	}
150	labelMap.put(uri, label);	15✔
151	}
152	}
153	}	3✔
154	} else if (apiString.startsWith("https://api.gbif.org/v1/species/suggest")) {	15✔
155	JSONArray responseArray = new JSONArray(respString);	15✔
156	for (int i = 0; i < responseArray.length(); i++) {	24✔
157	String uri = "https://www.gbif.org/species/" + responseArray.getJSONObject(i).getString("key");	21✔
158	String label = responseArray.getJSONObject(i).getString("scientificName");	18✔
159	if (!values.contains(uri)) {	12!
160	values.add(uri);	12✔
161	labelMap.put(uri, label);	15✔
162	}
163	}
164	} else if (apiString.startsWith("https://api.catalogueoflife.org/dataset/3LR/nameusage/search")) {	15✔
165	JSONArray responseArray = new JSONObject(respString).getJSONArray("result");	21✔
166	for (int i = 0; i < responseArray.length(); i++) {	24✔
167	String uri = "https://www.catalogueoflife.org/data/taxon/" + responseArray.getJSONObject(i).getString("id");	21✔
168	String label = responseArray.getJSONObject(i).getJSONObject("usage").getString("label");	24✔
169	if (!values.contains(uri)) {	12!
170	values.add(uri);	12✔
171	labelMap.put(uri, label);	15✔
172	}
173	}
174	} else if (apiString.startsWith("https://vodex.")) {	15✔
175	// TODO This is just a test and needs to be improved
176	JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");	27✔
177	for (int i = 0; i < responseArray.length(); i++) {	24✔
178	String uri = responseArray.getJSONObject(i).getString("id");	18✔
179	String label = responseArray.getJSONObject(i).getJSONArray("label").get(0).toString();	27✔
180	if (!values.contains(uri)) {	12!
181	values.add(uri);	12✔
182	labelMap.put(uri, label);	15✔
183	}
184	}
185	} else if (apiString.startsWith("https://api.ror.org/organizations")) {	15✔
186	// TODO This is just a test and needs to be improved
187	JSONArray responseArray = new JSONObject(respString).getJSONArray("items");	21✔
188	for (int i = 0; i < responseArray.length(); i++) {	24✔
189	String uri = responseArray.getJSONObject(i).getString("id");	18✔
190	JSONArray namesArray = responseArray.getJSONObject(i).getJSONArray("names");	18✔
191	if (namesArray.length() == 0) continue;	9!
192	String label = namesArray.getJSONObject(0).getString("value");	18✔
193	if (!values.contains(uri)) {	12!
194	values.add(uri);	12✔
195	labelMap.put(uri, label);	15✔
196	}
197	}
198	} else {	3✔
199	// TODO: create parseJsonApi() ?
200	boolean foundId = false;	6✔
201	JSONObject json = new JSONObject(respString);	15✔
202	for (String key : json.keySet()) {	33✔
203	if (values.size() > 9) break;	12!
204	if (!(json.get(key) instanceof JSONArray)) continue;	18✔
205	JSONArray a = json.getJSONArray(key);	12✔
206	for (int i = 0; i < a.length(); i++) {	24✔
207	if (values.size() > 9) break;	12!
208	if (!(a.get(i) instanceof JSONObject)) continue;	15!
209	JSONObject o = a.getJSONObject(i);	12✔
210	String uri = null;	6✔
211	for (String s : new String[]{"@id", "concepturi", "uri"}) {	87!
212	if (o.has(s)) {	12✔
213	uri = o.get(s).toString();	15✔
214	foundId = true;	6✔
215	break;	3✔
216	}
217	}
218	if (uri != null) {	6!
219	values.add(uri);	12✔
220	String label = "";	6✔
221	for (String s : new String[]{"prefLabel", "label"}) {	75!
222	if (o.has(s)) {	12✔
223	label = o.get(s).toString().replaceAll(" - ", " -- ");	24✔
224	break;	3✔
225	}
226	}
227	String desc = "";	6✔
228	for (String s : new String[]{"definition", "description"}) {	75!
229	if (o.has(s)) {	12✔
230	desc = o.get(s).toString();	15✔
231	break;	3✔
232	}
233	}
234	if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;	27!
235	labelMap.put(uri, label + desc);	21✔
236	}
237	}
238	}	3✔
239	if (foundId == false) {	6!
240	// ID key not found, try to get results for following format
241	// {result1: ["label 1", "label 2"], result2: ["label 3", "label 4"]}
242	// Aims to resolve https://name-resolution-sri.renci.org/docs#
243
244	// TODO: It seems this is triggered too often and adds 'https://identifiers.org/search' when it
245	// shouldn't. Manually filtering these out for now...
246	for (String key : json.keySet()) {	×
247	if (!(json.get(key) instanceof JSONArray)) continue;	×
248	if ("search".equals(key)) continue;	×
249	JSONArray labelArray = json.getJSONArray(key);	×
250	String uri = key;	×
251	String label = "";	×
252	String desc = "";	×
253	if (labelArray.length() > 0) label = labelArray.getString(0);	×
254	if (labelArray.length() > 1) desc = labelArray.getString(1);	×
255	if (desc.length() > 80) desc = desc.substring(0, 77) + "...";	×
256	if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;	×
257	// Quick fix to convert CURIE to URI, as Nanodash only accepts URIs here
258	if (!(uri.startsWith("http://") \|\| uri.startsWith("https://"))) {	×
259	uri = "https://identifiers.org/" + uri;	×
260	}
261	values.add(uri);	×
262	labelMap.put(uri, label + desc);	×
263	}	×
264	}
265	}
266	} catch (Exception ex) {	×
267	logger.error("Error fetching possible values from API: {}", apiString, ex);	×
268	}	3✔
269	}	3✔
270
271	private static void lookupNanopubNetwork(String apiString, String searchterm, Map<String, String> labelMap, List<String> values) {
272	String queryId = QueryApiAccess.FIND_THINGS;	6✔
273	if (apiString.startsWith("https://w3id.org/np/l/nanopub-query-1.1/api/")) {	12✔
274	queryId = apiString.replace("https://w3id.org/np/l/nanopub-query-1.1/api/", "");	15✔
275	if (queryId.contains("?")) queryId = queryId.substring(0, queryId.indexOf("?"));	33✔
276	}
277	Multimap<String, String> params = ArrayListMultimap.create();	6✔
278	if (apiString.contains("?")) {	12✔
279	List<NameValuePair> urlParams = URLEncodedUtils.parse(apiString.substring(apiString.indexOf("?") + 1), StandardCharsets.UTF_8);	30✔
280	for (NameValuePair p : urlParams) {	30✔
281	params.put(p.getName(), p.getValue());	21✔
282	}	3✔
283	}
284	GrlcQuery q = GrlcQuery.get(queryId);	9✔
285	if (q.getEndpoint().stringValue().endsWith("/text")) {	18✔
286	searchterm = expandSearchTerm(searchterm);	9✔
287	}
288	String queryParamName = "query";	6✔
289	if (q.getPlaceholdersList().size() == 1) {	15!
290	queryParamName = QueryParamField.getParamName(q.getPlaceholdersList().get(0));	×
291	}
292	params.put(queryParamName, searchterm);	15✔
293	ApiResponse result = ApiCache.retrieveResponseSync(new QueryRef(queryId, params), false);	24✔
294	int count = 0;	6✔
295	for (ApiResponseEntry r : result.getData()) {	33✔
296	String uri = r.get("thing");	12✔
297	values.add(uri);	12✔
298	String desc = r.get("description");	12✔
299	if (desc == null) desc = "";	12!
300	if (desc.length() > 80) desc = desc.substring(0, 77) + "...";	12!
301	if (!desc.isEmpty()) desc = " - " + desc;	9!
302	labelMap.put(uri, r.get("label") + desc);	27✔
303	count++;	3✔
304	if (count > 9) return;	9!
305	}	3✔
306	}	3✔
307
308	private static String expandSearchTerm(String searchTerm) {
309	String expanded = "";	6✔
310	boolean insideQuotes = false;	6✔
311	searchTerm = searchTerm.replaceAll("\\s+", " ").trim();	18✔
312	for (char c : searchTerm.toCharArray()) {	51✔
313	if (c == '\n') {	9!
314	continue;	×
315	} else if (c == '"') {	9✔
316	expanded += '"';	9✔
317	insideQuotes = !insideQuotes;	21✔
318	} else if (c == ' ') {	9✔
319	if (insideQuotes) {	6✔
320	expanded += ' ';	12✔
321	} else {
322	expanded += '\n';	12✔
323	}
324	} else if (("" + c).matches("\\w") \|\| c == '-' \|\| c == '_') {	15!
325	expanded += c;	15✔
326	} else {
327	if (insideQuotes) {	×
328	expanded += ' ';	×
329	} else {
330	expanded += '\n';	×
331	}
332	}
333	}
334	String extra = "*";	6✔
335	expanded = expanded.replaceAll("\\n+", "\n").replaceAll("\"", "\\\\\\\"").trim();	27✔
336	if (expanded.endsWith("\"") \|\| insideQuotes) extra = "";	24!
337	return "( " + Strings.join(" AND ", expanded.split("\n")) + extra + " )";	24✔
338	}
339
340	}

knowledgepixels / nanodash / 24565015084

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