23112508226

Committed 15 Mar 2026 02:37PM UTC coverage: 15.984% (+0.2%) from 15.811%

Build # 23112508226

Build Type

Pull #402

github

Committed by

web-flow

Commit Message

Merge b1ffd3d2f into 7b510582a

Pull Request Pull Request #402: Fix unbounded memory growth and resource exhaustion

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0.0

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?")) {
                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;
                }
                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?")) {
                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) {
                        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 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);	×
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");	×
52	for (int i = 0; i < resultsArray.length(); i++) {	×
53	JSONObject resultObject = resultsArray.getJSONObject(i);	×
54	// Get the nanopub URI
55	String uri = resultObject.getJSONObject("thing").getString("value");	×
56	// Get the string which matched with the search term
57	String label = resultObject.getJSONObject("label").getString("value");	×
58	values.add(uri);	×
59	labelMap.put(uri, label);	×
60	}
61	}	×
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?")) {	×
75	String queryId = QueryApiAccess.FIND_THINGS;	×
76	if (apiString.startsWith("https://w3id.org/np/l/nanopub-query-1.1/api/")) {	×
77	queryId = apiString.replace("https://w3id.org/np/l/nanopub-query-1.1/api/", "");	×
78	if (queryId.contains("?")) queryId = queryId.substring(0, queryId.indexOf("?"));	×
79	}
80	Multimap<String, String> params = ArrayListMultimap.create();	×
81	if (apiString.contains("?")) {	×
82	List<NameValuePair> urlParams = URLEncodedUtils.parse(apiString.substring(apiString.indexOf("?") + 1), StandardCharsets.UTF_8);	×
83	for (NameValuePair p : urlParams) {	×
84	params.put(p.getName(), p.getValue());	×
85	}	×
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 = ApiCache.retrieveResponseSync(new QueryRef(queryId, params), false);	×
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	EntityUtils.consume(resp.getEntity());	×
130	HttpPost post = new HttpPost(apiString + URLEncoder.encode(searchterm, StandardCharsets.UTF_8.toString()));	×
131	resp = client.execute(post);	×
132	}
133	// TODO: support other content types (CSV, XML, ...)
134	// System.err.println(resp.getHeaders("Content-Type")[0]);
135	try (InputStream in = resp.getEntity().getContent()) {	×
136	respString = IOUtils.toString(in, StandardCharsets.UTF_8);	×
137	}
138	}
139	// System.out.println(respString);
140
141	if (apiString.startsWith("https://w3id.org/np/l/nanopub-query") \|\| apiString.startsWith("https://grlc.") \|\| apiString.contains("/sparql?")) {	×
142	JSONArray resultsArray = new JSONObject(respString).getJSONObject("results").getJSONArray("bindings");	×
143	for (int i = 0; i < resultsArray.length(); i++) {	×
144	JSONObject resultObject = resultsArray.getJSONObject(i);	×
145	// Get the nanopub URI
146	String uri = resultObject.getJSONObject("thing").getString("value");	×
147	// Get the string which matched with the search term
148	String label = resultObject.getJSONObject("label").getString("value");	×
149	values.add(uri);	×
150	labelMap.put(uri, label);	×
151	}
152	} else if (apiString.startsWith("https://www.ebi.ac.uk/ols/api/select")) {	×
153	// Resolve EBI Ontology Lookup Service
154	// e.g. https://www.ebi.ac.uk/ols/api/select?q=interacts%20with
155	// response.docs.[].iri/label
156	JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");	×
157	for (int i = 0; i < responseArray.length(); i++) {	×
158	String uri = responseArray.getJSONObject(i).getString("iri");	×
159	String label = responseArray.getJSONObject(i).getString("label");	×
160	try {
161	label += " - " + responseArray.getJSONObject(i).getJSONArray("description").getString(0);	×
162	} catch (Exception ex) {	×
163	logger.error("No description found for {}", uri, ex);	×
164	}	×
165	if (!values.contains(uri)) {	×
166	values.add(uri);	×
167	labelMap.put(uri, label);	×
168	}
169	}
170	} else if (apiString.startsWith("https://api.openaire.eu/graph/v")) {	×
171	String type = apiString.replaceFirst("^https://api\\.openaire\\.eu/graph/(v[0-9]+/[a-zA-Z]+).*$", "$1");	×
172	for (Object obj : new JSONObject(respString).getJSONArray("results")) {	×
173	if (obj instanceof JSONObject jsonObj) {	×
174	String uri = "https://api.openaire.eu/graph/" + type + "/" + jsonObj.getString("id");	×
175	if (!values.contains(uri)) {	×
176	values.add(uri);	×
177	String label = uri;	×
178	if (jsonObj.has("mainTitle")) {	×
179	label = jsonObj.getString("mainTitle");	×
180	} else if (jsonObj.has("legalShortName")) {	×
181	label = jsonObj.getString("legalShortName");	×
182	} else if (jsonObj.has("officialName")) {	×
183	label = jsonObj.getString("officialName");	×
184	} else if (jsonObj.has("title")) {	×
185	label = jsonObj.getString("title");	×
186	} else if (jsonObj.has("familyName")) {	×
187	label = jsonObj.getString("familyName");	×
188	if (jsonObj.has("givenName")) {	×
189	label = jsonObj.getString("givenName") + " " + label;	×
190	}
191	}
192	labelMap.put(uri, label);	×
193	}
194	}
195	}	×
196	} else if (apiString.startsWith("https://api.gbif.org/v1/species/suggest")) {	×
197	JSONArray responseArray = new JSONArray(respString);	×
198	for (int i = 0; i < responseArray.length(); i++) {	×
199	String uri = "https://www.gbif.org/species/" + responseArray.getJSONObject(i).getString("key");	×
200	String label = responseArray.getJSONObject(i).getString("scientificName");	×
201	if (!values.contains(uri)) {	×
202	values.add(uri);	×
203	labelMap.put(uri, label);	×
204	}
205	}
206	} else if (apiString.startsWith("https://api.catalogueoflife.org/dataset/3LR/nameusage/search")) {	×
207	JSONArray responseArray = new JSONObject(respString).getJSONArray("result");	×
208	for (int i = 0; i < responseArray.length(); i++) {	×
209	String uri = "https://www.catalogueoflife.org/data/taxon/" + responseArray.getJSONObject(i).getString("id");	×
210	String label = responseArray.getJSONObject(i).getJSONObject("usage").getString("label");	×
211	if (!values.contains(uri)) {	×
212	values.add(uri);	×
213	labelMap.put(uri, label);	×
214	}
215	}
216	} else if (apiString.startsWith("https://vodex.")) {	×
217	// TODO This is just a test and needs to be improved
218	JSONArray responseArray = new JSONObject(respString).getJSONObject("response").getJSONArray("docs");	×
219	for (int i = 0; i < responseArray.length(); i++) {	×
220	String uri = responseArray.getJSONObject(i).getString("id");	×
221	String label = responseArray.getJSONObject(i).getJSONArray("label").get(0).toString();	×
222	if (!values.contains(uri)) {	×
223	values.add(uri);	×
224	labelMap.put(uri, label);	×
225	}
226	}
227	} else if (apiString.startsWith("https://api.ror.org/organizations")) {	×
228	// TODO This is just a test and needs to be improved
229	JSONArray responseArray = new JSONObject(respString).getJSONArray("items");	×
230	for (int i = 0; i < responseArray.length(); i++) {	×
231	String uri = responseArray.getJSONObject(i).getString("id");	×
232	JSONArray namesArray = responseArray.getJSONObject(i).getJSONArray("names");	×
233	if (namesArray.length() == 0) continue;	×
234	String label = namesArray.getJSONObject(0).getString("value");	×
235	if (!values.contains(uri)) {	×
236	values.add(uri);	×
237	labelMap.put(uri, label);	×
238	}
239	}
240	} else {	×
241	// TODO: create parseJsonApi() ?
242	boolean foundId = false;	×
243	JSONObject json = new JSONObject(respString);	×
244	for (String key : json.keySet()) {	×
245	if (values.size() > 9) break;	×
246	if (!(json.get(key) instanceof JSONArray)) continue;	×
247	JSONArray a = json.getJSONArray(key);	×
248	for (int i = 0; i < a.length(); i++) {	×
249	if (values.size() > 9) break;	×
250	if (!(a.get(i) instanceof JSONObject)) continue;	×
251	JSONObject o = a.getJSONObject(i);	×
252	String uri = null;	×
253	for (String s : new String[]{"@id", "concepturi", "uri"}) {	×
254	if (o.has(s)) {	×
255	uri = o.get(s).toString();	×
256	foundId = true;	×
257	break;	×
258	}
259	}
260	if (uri != null) {	×
261	values.add(uri);	×
262	String label = "";	×
263	for (String s : new String[]{"prefLabel", "label"}) {	×
264	if (o.has(s)) {	×
265	label = o.get(s).toString().replaceAll(" - ", " -- ");	×
266	break;	×
267	}
268	}
269	String desc = "";	×
270	for (String s : new String[]{"definition", "description"}) {	×
271	if (o.has(s)) {	×
272	desc = o.get(s).toString();	×
273	break;	×
274	}
275	}
276	if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;	×
277	labelMap.put(uri, label + desc);	×
278	}
279	}
280	}	×
281	if (foundId == false) {	×
282	// ID key not found, try to get results for following format
283	// {result1: ["label 1", "label 2"], result2: ["label 3", "label 4"]}
284	// Aims to resolve https://name-resolution-sri.renci.org/docs#
285
286	// TODO: It seems this is triggered too often and adds 'https://identifiers.org/search' when it
287	// shouldn't. Manually filtering these out for now...
288	for (String key : json.keySet()) {	×
289	if (!(json.get(key) instanceof JSONArray)) continue;	×
290	if ("search".equals(key)) continue;	×
291	JSONArray labelArray = json.getJSONArray(key);	×
292	String uri = key;	×
293	String label = "";	×
294	String desc = "";	×
295	if (labelArray.length() > 0) label = labelArray.getString(0);	×
296	if (labelArray.length() > 1) desc = labelArray.getString(1);	×
297	if (desc.length() > 80) desc = desc.substring(0, 77) + "...";	×
298	if (!label.isEmpty() && !desc.isEmpty()) desc = " - " + desc;	×
299	// Quick fix to convert CURIE to URI, as Nanodash only accepts URIs here
300	if (!(uri.startsWith("http://") \|\| uri.startsWith("https://"))) {	×
301	uri = "https://identifiers.org/" + uri;	×
302	}
303	values.add(uri);	×
304	labelMap.put(uri, label + desc);	×
305	}	×
306	}
307	}
308	} catch (Exception ex) {	×
309	logger.error("Error fetching possible values from API: {}", apiString, ex);	×
310	}	×
311	}	×
312
313	private static String expandSearchTerm(String searchTerm) {
314	String expanded = "";	×
315	boolean insideQuotes = false;	×
316	searchTerm = searchTerm.replaceAll("\\s+", " ").trim();	×
317	for (char c : searchTerm.toCharArray()) {	×
318	if (c == '\n') {	×
319	continue;	×
320	} else if (c == '"') {	×
321	expanded += '"';	×
322	insideQuotes = !insideQuotes;	×
323	} else if (c == ' ') {	×
324	if (insideQuotes) {	×
325	expanded += ' ';	×
326	} else {
327	expanded += '\n';	×
328	}
329	} else if (("" + c).matches("\\w") \|\| c == '-' \|\| c == '_') {	×
330	expanded += c;	×
331	} else {
332	if (insideQuotes) {	×
333	expanded += ' ';	×
334	} else {
335	expanded += '\n';	×
336	}
337	}
338	}
339	String extra = "*";	×
340	expanded = expanded.replaceAll("\\n+", "\n").replaceAll("\"", "\\\\\\\"").trim();	×
341	if (expanded.endsWith("\"") \|\| insideQuotes) extra = "";	×
342	return "( " + Strings.join(" AND ", expanded.split("\n")) + extra + " )";	×
343	}
344
345	}

knowledgepixels / nanodash / 23112508226

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