Examples with JSONParser org.json.simple.parser.JSONParser used on opensource projects

Example 26 with JSONParser

use of org.json.simple.parser.JSONParser in project spatial-portal by AtlasOfLivingAustralia.

the class CommonData method initJournalmap.

private static void initJournalmap() {
    if (journalMapArticles != null && journalMapArticles.size() > 0) {
        return;
    }
    journalMapArticles = new ArrayList<JSONObject>();
    journalMapLocations = new ArrayList<JournalMapLocation>();
    try {
        String journalmapUrl = CommonData.getSettings().getProperty("journalmap.url", null);
        String journalmapKey = CommonData.getSettings().getProperty("journalmap.api_key", null);
        //try disk cache
        File jaFile = new File("/data/webportal/journalmapArticles.json");
        if (jaFile.exists()) {
            JSONParser jp = new JSONParser();
            JSONArray ja = (JSONArray) jp.parse(FileUtils.readFileToString(jaFile));
            for (int i = 0; i < ja.size(); i++) {
                journalMapArticles.add((JSONObject) ja.get(i));
            }
        } else if (journalmapKey != null && !journalmapKey.isEmpty()) {
            int page = 1;
            int maxpage = 0;
            List<String> publicationsIds = new ArrayList<String>();
            while (page == 1 || page <= maxpage) {
                HttpClient client = new HttpClient();
                String url = journalmapUrl + "api/publications.json?version=1.0&key=" + journalmapKey + "&page=" + page;
                page = page + 1;
                LOGGER.debug("journalmap url: " + url);
                GetMethod get = new GetMethod(url);
                int result = client.executeMethod(get);
                //update maxpage
                maxpage = Integer.parseInt(get.getResponseHeader("X-Pages").getValue());
                //cache
                JSONParser jp = new JSONParser();
                JSONArray jcollection = (JSONArray) jp.parse(get.getResponseBodyAsString());
                for (int i = 0; i < jcollection.size(); i++) {
                    if (((JSONObject) jcollection.get(i)).containsKey("id")) {
                        publicationsIds.add(((JSONObject) jcollection.get(i)).get("id").toString());
                        LOGGER.debug("found publication: " + ((JSONObject) jcollection.get(i)).get("id").toString() + ", article_count: " + ((JSONObject) jcollection.get(i)).get("articles_count").toString());
                    }
                }
            }
            for (String publicationsId : publicationsIds) {
                //allow for collection failure
                try {
                    page = 1;
                    maxpage = 0;
                    while (page == 1 || page <= maxpage) {
                        HttpClient client = new HttpClient();
                        String url = journalmapUrl + "api/articles.json?version=1.0&key=" + journalmapKey + "&page=" + page + "&publication_id=" + publicationsId;
                        page = page + 1;
                        LOGGER.debug("journalmap url: " + url);
                        GetMethod get = new GetMethod(url);
                        int result = client.executeMethod(get);
                        //update maxpage
                        maxpage = Integer.parseInt(get.getResponseHeader("X-Pages").getValue());
                        //cache
                        JSONParser jp = new JSONParser();
                        JSONArray jarticles = (JSONArray) jp.parse(get.getResponseBodyAsString());
                        for (int j = 0; j < jarticles.size(); j++) {
                            JSONObject o = (JSONObject) jarticles.get(j);
                            if (o.containsKey("locations")) {
                                journalMapArticles.add(o);
                            }
                        }
                    }
                } catch (Exception e) {
                    LOGGER.error("journalmap - failure to get articles from publicationsId: " + publicationsId);
                }
            }
            //save to disk cache
            FileWriter fw = new FileWriter(jaFile);
            JSONValue.writeJSONString(journalMapArticles, fw);
            fw.flush();
            fw.close();
        }
    } catch (Exception e) {
        LOGGER.error("error initialising journalmap data", e);
    }
    //construct locations list
    for (int i = 0; i < journalMapArticles.size(); i++) {
        JSONArray locations = (JSONArray) journalMapArticles.get(i).get("locations");
        for (int j = 0; j < locations.size(); j++) {
            JSONObject l = (JSONObject) locations.get(j);
            double longitude = Double.parseDouble(l.get("longitude").toString());
            double latitude = Double.parseDouble(l.get("latitude").toString());
            journalMapLocations.add(new JournalMapLocation(longitude, latitude, i));
        }
    }
}

Example 27 with JSONParser

use of org.json.simple.parser.JSONParser in project spatial-portal by AtlasOfLivingAustralia.

the class BiocacheQuery method getScientificNameRank.

public static String getScientificNameRank(String lsid) {
    String snUrl = "true".equalsIgnoreCase(CommonData.getSettings().getProperty("new.bie")) ? CommonData.getBieServer() + BIE_SPECIES_WS + lsid + ".json" : CommonData.getBieServer() + BIE_SPECIES + lsid + ".json";
    LOGGER.debug(snUrl);
    try {
        HttpClient client = new HttpClient();
        GetMethod get = new GetMethod(snUrl);
        get.addRequestHeader(StringConstants.CONTENT_TYPE, StringConstants.APPLICATION_JSON);
        client.executeMethod(get);
        String slist = get.getResponseBodyAsString();
        JSONParser jp = new JSONParser();
        JSONObject jo = (JSONObject) jp.parse(slist);
        String scientficName = ((JSONObject) jo.get("taxonConcept")).get("nameString").toString();
        String r = ((JSONObject) jo.get("taxonConcept")).get("rankString").toString();
        LOGGER.debug("Arrays.binarySearch(COMMON_TAXON_RANKS, rank): " + Arrays.binarySearch(COMMON_TAXON_RANKS, r));
        if (Arrays.binarySearch(COMMON_TAXON_RANKS, r) > -1) {
            r = StringConstants.TAXON;
        }
        return scientficName + "," + r;
    } catch (Exception e) {
        LOGGER.error("error getting scientific name:" + snUrl, e);
    }
    return StringConstants.OCCURRENCES;
}

Example 28 with JSONParser

use of org.json.simple.parser.JSONParser in project spatial-portal by AtlasOfLivingAustralia.

the class BiocacheQuery method retrieveCustomFields.

private List<String> retrieveCustomFields() {
    List<String> customFields = new ArrayList<String>();
    //look up facets
    final String jsonUri = biocacheServer + "/upload/dynamicFacets?q=" + getFullQ(true) + "&qc=" + getQc();
    try {
        HttpClient client = new HttpClient();
        GetMethod get = new GetMethod(jsonUri);
        get.addRequestHeader(StringConstants.CONTENT_TYPE, StringConstants.APPLICATION_JSON);
        client.executeMethod(get);
        String slist = get.getResponseBodyAsString();
        JSONParser jp = new JSONParser();
        JSONArray ja = (JSONArray) jp.parse(slist);
        for (Object arrayElement : ja) {
            JSONObject jsonObject = (JSONObject) arrayElement;
            String facetName = jsonObject.get(StringConstants.NAME).toString();
            if (!facetName.endsWith("_RNG")) {
                customFields.add(facetName);
            }
        }
    } catch (Exception e) {
        LOGGER.error("error loading custom facets for: " + jsonUri, e);
    }
    return customFields;
}

Example 29 with JSONParser

use of org.json.simple.parser.JSONParser in project spatial-portal by AtlasOfLivingAustralia.

the class BiocacheQuery method endemicSpeciesList.

public String endemicSpeciesList() {
    if (endemicSpeciesList != null) {
        return endemicSpeciesList;
    }
    if (CommonData.getSettings().containsKey("endemic.sp.method") && CommonData.getSettings().getProperty("endemic.sp.method").equals("true")) {
        String speciesList = speciesList();
        //can get species list counts as "kosher:true" or "kosher:*" only
        Map speciesCounts;
        if (getGeospatialKosher()[1]) {
            //[1] is 'include kosher:false'
            speciesCounts = CommonData.getSpeciesListCounts(false);
        } else {
            speciesCounts = CommonData.getSpeciesListCountsKosher(false);
        }
        StringBuilder sb = new StringBuilder();
        int speciesCol = 0;
        int countCol = 11;
        try {
            CSVReader csv = new CSVReader(new StringReader(speciesList));
            String[] row;
            int currentPos = 0;
            int nextPos = speciesList.indexOf('\n', currentPos + 1);
            //header
            sb.append(speciesList.substring(currentPos, nextPos));
            //header
            csv.readNext();
            while ((row = csv.readNext()) != null) {
                //add if species is not present elsewhere
                Long c = (Long) speciesCounts.get(row[speciesCol]);
                if (c != null && c <= Long.parseLong(row[countCol])) {
                    if (nextPos > speciesList.length()) {
                        nextPos = speciesList.length();
                    }
                    sb.append(speciesList.substring(currentPos, nextPos));
                } else if (c == null) {
                    LOGGER.error("failed to find species_guid: " + row[speciesCol] + " in CommonData.getSpeciesListCounts()");
                }
                currentPos = nextPos;
                nextPos = speciesList.indexOf('\n', currentPos + 1);
            }
        } catch (Exception e) {
            LOGGER.error("failed generating endemic species list", e);
        }
        endemicSpeciesList = sb.toString();
    } else {
        forMapping = true;
        if (paramId == null)
            makeParamId();
        HttpClient client = new HttpClient();
        String url = biocacheServer + ENDEMIC_LIST + paramId + "?facets=names_and_lsid";
        LOGGER.debug(url);
        GetMethod get = new GetMethod(url);
        try {
            client.executeMethod(get);
            JSONParser jp = new JSONParser();
            JSONArray ja = (JSONArray) jp.parse(get.getResponseBodyAsString());
            //extract endemic matches from the species list
            String speciesList = speciesList();
            StringBuilder sb = new StringBuilder();
            int idx = speciesList.indexOf('\n');
            if (idx > 0) {
                sb.append(speciesList.substring(0, idx));
            }
            for (int j = 0; j < ja.size(); j++) {
                JSONObject jo = (JSONObject) ja.get(j);
                if (jo.containsKey("label")) {
                    idx = speciesList.indexOf("\n" + jo.get("label") + ",");
                    if (idx > 0) {
                        int lineEnd = speciesList.indexOf('\n', idx + 1);
                        if (lineEnd < 0)
                            lineEnd = speciesList.length();
                        sb.append(speciesList.substring(idx, lineEnd));
                    }
                }
            }
            endemicSpeciesList = sb.toString();
        } catch (Exception e) {
            LOGGER.error("error getting endemic species result", e);
        }
    }
    return endemicSpeciesList;
}

Example 30 with JSONParser

use of org.json.simple.parser.JSONParser in project spatial-portal by AtlasOfLivingAustralia.

the class RemoteLogger method getLogCSV.

public JSONObject getLogCSV() {
    init();
    try {
        if (Util.isLoggedIn()) {
            String url = loggerService + "/app/types/tool.json?" + "email=" + URLEncoder.encode(Util.getUserEmail(), StringConstants.UTF_8) + "&appid=" + URLEncoder.encode(appid, StringConstants.UTF_8) + "&api_key=" + URLEncoder.encode(CommonData.getSettings().getProperty("api_key"), StringConstants.UTF_8);
            HttpClient client = new HttpClient();
            GetMethod get = new GetMethod(url);
            get.addRequestHeader(StringConstants.ACCEPT, StringConstants.APPLICATION_JSON);
            client.executeMethod(get);
            LOGGER.debug("get: " + url + ", response: " + get.getResponseBodyAsString());
            JSONParser jp = new JSONParser();
            return (JSONObject) jp.parse(get.getResponseBodyAsString());
        }
    } catch (Exception e) {
        LOGGER.error("Error getting logging information from server:", e);
    }
    return null;
}