Examples with CSVReader au.com.bytecode.opencsv.CSVReader used on opensource projects

Example 21 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project spatial-portal by AtlasOfLivingAustralia.

the class CommonData method getSpeciesListCountsKosher.

public static Map getSpeciesListCountsKosher(boolean refresh) {
    if (speciesListCountsKosher == null || refresh) {
        Map m = new HashMap();
        HttpClient client = new HttpClient();
        String url = biocacheServer + "/occurrences/facets/download?facets=species_guid&count=true" + "&q=geospatial_kosher:true";
        LOGGER.debug(url);
        GetMethod get = new GetMethod(url);
        try {
            client.executeMethod(get);
            CSVReader csv = new CSVReader(new BufferedReader(new InputStreamReader(get.getResponseBodyAsStream())));
            String[] row;
            //skip header
            csv.readNext();
            while ((row = csv.readNext()) != null) {
                try {
                    m.put(row[0], Long.parseLong(row[1]));
                } catch (Exception e) {
                    LOGGER.error("error getting species_guid,count (kosher): " + url, e);
                }
            }
        } catch (Exception e) {
            LOGGER.error("error getting species list from: " + url);
        }
        speciesListCountsUpdatedKosher = System.currentTimeMillis();
        speciesListCountsKosher = m;
    }
    return speciesListCountsKosher;
}

Example 22 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project spatial-portal by AtlasOfLivingAustralia.

the class CommonData method getSpeciesListCounts.

public static Map getSpeciesListCounts(boolean refresh) {
    if (speciesListCounts == null || refresh) {
        Map m = new HashMap();
        HttpClient client = new HttpClient();
        String url = biocacheServer + "/occurrences/facets/download?facets=species_guid&count=true" + "&q=geospatial_kosher:*";
        LOGGER.debug(url);
        GetMethod get = new GetMethod(url);
        try {
            client.executeMethod(get);
            CSVReader csv = new CSVReader(new BufferedReader(new InputStreamReader(get.getResponseBodyAsStream())));
            String[] row;
            //skip header
            csv.readNext();
            while ((row = csv.readNext()) != null) {
                try {
                    m.put(row[0], Long.parseLong(row[1]));
                } catch (Exception e) {
                    LOGGER.error("error getting species_guid,count: " + url, e);
                }
            }
        } catch (Exception e) {
            LOGGER.error("error getting species list from: " + url);
        }
        speciesListCountsUpdated = System.currentTimeMillis();
        speciesListCounts = m;
    }
    return speciesListCounts;
}

Example 23 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project spatial-portal by AtlasOfLivingAustralia.

the class BiocacheQuery method speciesList.

/**
     * Get species list for this query.
     *
     * @return species list as String containing CSV.
     */
@Override
public String speciesList() {
    if (speciesList != null) {
        return speciesList;
    }
    HttpClient client = new HttpClient();
    String url = biocacheServer + SPECIES_LIST_SERVICE_CSV + "&q=" + getQ() + getQc();
    LOGGER.debug(url);
    GetMethod get = new GetMethod(url);
    try {
        client.executeMethod(get);
        speciesList = get.getResponseBodyAsString();
        //add 'Other' correction and add additional columns
        List<String> header = CommonData.getSpeciesListAdditionalColumnsHeader();
        StringBuilder newlist = new StringBuilder();
        int total = getOccurrenceCount();
        CSVReader csv = new CSVReader(new StringReader(speciesList));
        String[] line;
        int count = 0;
        int lastpos = 0;
        while ((line = csv.readNext()) != null) {
            int nextpos = speciesList.indexOf('\n', lastpos + 1);
            if (nextpos < 0)
                nextpos = speciesList.length();
            newlist.append(speciesList.substring(lastpos, nextpos));
            List<String> list = header;
            if (lastpos != 0) {
                list = CommonData.getSpeciesListAdditionalColumns(header, line[0]);
            }
            for (int i = 0; i < list.size(); i++) {
                newlist.append(",\"").append(list.get(i).replace("\"", "\"\"").replace("\\", "\\\\")).append("\"");
            }
            lastpos = nextpos;
            try {
                count += Integer.parseInt(line[line.length - 1]);
            } catch (Exception e) {
            }
        }
        if (total - count > 0) {
            String correction = "\n,,,,,,,,,,Other (not species rank)," + (total - count);
            newlist.append(correction);
        }
        speciesList = newlist.toString();
    } catch (Exception e) {
        LOGGER.error("error getting species list from: " + url);
    }
    return speciesList;
}

Example 24 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project spatial-portal by AtlasOfLivingAustralia.

the class SamplingDownloadUtil method downloadSecond.

public static byte[] downloadSecond(MapComposer mc, Query downloadSecondQuery, String[] downloadSecondLayers, String[] downloadSecondLayersDN) {
    LOGGER.debug("attempting to sample biocache records with analysis layers: " + downloadSecondQuery);
    if (downloadSecondQuery != null) {
        try {
            List<QueryField> fields = new ArrayList<QueryField>();
            fields.add(new QueryField(downloadSecondQuery.getRecordIdFieldName()));
            fields.add(new QueryField(downloadSecondQuery.getRecordLongitudeFieldName()));
            fields.add(new QueryField(downloadSecondQuery.getRecordLatitudeFieldName()));
            String results = downloadSecondQuery.sample(fields);
            if (results != null) {
                CSVReader csvreader = new CSVReader(new StringReader(results));
                List<String[]> csv = csvreader.readAll();
                csvreader.close();
                int longitudeColumn = Util.findInArray(downloadSecondQuery.getRecordLongitudeFieldDisplayName(), csv.get(0));
                int latitudeColumn = Util.findInArray(downloadSecondQuery.getRecordLatitudeFieldDisplayName(), csv.get(0));
                int idColumn = Util.findInArray(downloadSecondQuery.getRecordIdFieldDisplayName(), csv.get(0));
                double[] points = new double[(csv.size() - 1) * 2];
                String[] ids = new String[csv.size() - 1];
                int pos = 0;
                for (int i = 1; i < csv.size(); i++) {
                    try {
                        points[pos] = Double.parseDouble(csv.get(i)[longitudeColumn]);
                        points[pos + 1] = Double.parseDouble(csv.get(i)[latitudeColumn]);
                    } catch (Exception e) {
                        points[pos] = Double.NaN;
                        points[pos + 1] = Double.NaN;
                    }
                    ids[pos / 2] = csv.get(i)[idColumn];
                    pos += 2;
                }
                double[][] p = new double[points.length / 2][2];
                for (int i = 0; i < points.length; i += 2) {
                    p[i / 2][0] = points[i];
                    p[i / 2][1] = points[i + 1];
                }
                List<String> layers = new ArrayList<String>();
                StringBuilder sb = new StringBuilder();
                sb.append("id,longitude,latitude");
                for (int i = 0; i < downloadSecondLayers.length; i++) {
                    String layer = downloadSecondLayers[i];
                    sb.append(",");
                    String name = downloadSecondLayersDN[i];
                    sb.append(name);
                    layers.add(CommonData.getLayerFacetName(layer));
                }
                List<String[]> sample = Sampling.sampling(layers, p);
                if (!sample.isEmpty()) {
                    for (int j = 0; j < sample.get(0).length; j++) {
                        sb.append("\n");
                        sb.append(ids[j]).append(",").append(p[j][0]).append(",").append(p[j][1]);
                        for (int i = 0; i < sample.size(); i++) {
                            sb.append(",").append(sample.get(i)[j]);
                        }
                    }
                }
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                ZipOutputStream zos = new ZipOutputStream(baos);
                ZipEntry anEntry = new ZipEntry("analysis_output_intersect.csv");
                zos.putNextEntry(anEntry);
                zos.write(sb.toString().getBytes());
                zos.close();
                return baos.toByteArray();
            }
        } catch (Exception e) {
            LOGGER.error("error downloading samping records", e);
        }
    }
    return null;
}

Example 25 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project spatial-portal by AtlasOfLivingAustralia.

the class MapComposer method openChecklistSpecies.

void openChecklistSpecies(String lsids, String wkt, boolean mapIfOnlyOne) {
    try {
        //species checklists
        String[] finallist = Util.getDistributionsOrChecklists(StringConstants.CHECKLISTS, wkt, lsids, null);
        //open for optional mapping of areas
        if (finallist.length > 1) {
            if (mapIfOnlyOne && finallist.length == 2) {
                try {
                    String[] row;
                    CSVReader csv = new CSVReader(new StringReader(finallist[1]));
                    row = csv.readNext();
                    csv.close();
                    if (getMapLayerWMS(CommonData.getSpeciesChecklistWMSFromSpcode(row[0])[1]) == null) {
                        //map it
                        String[] mapping = CommonData.getSpeciesChecklistWMSFromSpcode(row[0]);
                        String displayName = mapping[0] + " area";
                        if (row[11] != null && row[11].length() > 0) {
                            displayName = row[11];
                        }
                        String layerName = getNextAreaLayerName(row[0] + " area");
                        String html = Util.getMetadataHtmlForDistributionOrChecklist(row[0], row, layerName);
                        MapLayer ml = getMapComposer().addWMSLayer(layerName, displayName, mapping[1], 0.6f, html, null, LayerUtilitiesImpl.WKT, null, null);
                        ml.setSPCode(row[0]);
                        setupMapLayerAsDistributionArea(ml);
                    }
                } catch (Exception e) {
                    LOGGER.error("error opening checklist species", e);
                }
            } else {
                if (hasFellow(StringConstants.DISTRIBUTION_RESULTS)) {
                    getFellowIfAny(StringConstants.DISTRIBUTION_RESULTS).detach();
                }
                Map params = new HashMap();
                params.put(StringConstants.TITLE, "Checklist species");
                params.put(StringConstants.SIZE, String.valueOf(finallist.length - 1));
                params.put(StringConstants.TABLE, finallist);
                Window window = (Window) Executions.createComponents("WEB-INF/zul/results/AnalysisDistributionResults.zul", this, params);
                try {
                    window.setParent(this);
                    window.doModal();
                } catch (Exception e) {
                    LOGGER.error("error opening checklist species dialog", e);
                }
            }
        }
    } catch (Exception e) {
        LOGGER.error("error opening distribution area dialog", e);
    }
}