17397874744

Committed 02 Sep 2025 08:30AM UTC coverage: 12.028% (-0.002%) from 12.03%

Build # 17397874744

Build Type

push

github

Committed by

tkuhn

Commit Message

Set user agent for lookup API calls (now enforced by WikiData)

Run Details

330 of 3850 branches covered (8.57%)

Branch coverage included in aggregate %.

958 of 6858 relevant lines covered (13.97%)

0.62 hits per line

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

0.0

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

package com.knowledgepixels.nanodash;

import com.beust.jcommander.Strings;
import com.github.openjson.JSONArray;
import com.github.openjson.JSONObject;
import com.knowledgepixels.nanodash.component.QueryParamField;
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.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.nanopub.extra.services.ApiResponse;
import org.nanopub.extra.services.ApiResponseEntry;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

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

knowledgepixels / nanodash / 17397874744

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