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

Example 11 with CSVReader

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

the class PhylogeneticDiversityListResults method evalArea.

private void evalArea(SelectedArea sa) {
    try {
        Query sq = QueryUtil.queryFromSelectedArea(selectedQuery, sa, null, false, null);
        CSVReader r = new CSVReader(new StringReader(sq.speciesList()));
        JSONArray ja = new JSONArray();
        for (String[] s : r.readAll()) {
            ja.add(s[1]);
        }
        //call pd with specieslist=ja.toString()
        String url = CommonData.getSettings().getProperty(CommonData.PHYLOLIST_URL) + "/phylo/getPD";
        NameValuePair[] params = new NameValuePair[2];
        params[0] = new NameValuePair("noTreeText", StringConstants.TRUE);
        params[1] = new NameValuePair("speciesList", ja.toString());
        JSONParser jp = new JSONParser();
        JSONArray pds = (JSONArray) jp.parse(Util.readUrlPost(url, params));
        Map<String, String> pdrow = new HashMap<String, String>();
        Map<String, JSONArray> speciesRow = new HashMap<String, JSONArray>();
        for (int j = 0; j < pds.size(); j++) {
            String tree = "" + ((JSONObject) pds.get(j)).get(StringConstants.STUDY_ID);
            pdrow.put(tree, ((JSONObject) pds.get(j)).get("pd").toString());
            speciesRow.put(tree, (JSONArray) ((JSONObject) pds.get(j)).get("taxaRecognised"));
            //maxPD retrieval
            String maxPd = ((JSONObject) pds.get(j)).get("maxPd").toString();
            for (int k = 0; k < selectedTrees.size(); k++) {
                if (((Map<String, String>) selectedTrees.get(k)).get(StringConstants.STUDY_ID).equals(tree)) {
                    ((Map<String, String>) selectedTrees.get(k)).put("maxPd", maxPd);
                }
            }
        }
        areaPds.add(pdrow);
        areaSpeciesMatches.add(speciesRow);
    } catch (Exception e) {
        LOGGER.error("failed processing a pd for a selected area.", e);
    }
}

Example 12 with CSVReader

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

the class PhylogeneticDiversityListResults method makeCSV.

private void makeCSV() {
    StringBuilder sb = new StringBuilder();
    //header
    sb.append("Area Name,Area (sq km),PD,Proportional PD (PD / Tree PD),");
    sb.append("Species,Proportional Species (Species / Tree Species),Tree Name,Tree ID,DOI,Study Name,Notes,Tree PD");
    //rows
    for (int j = 0; j < selectedTrees.size(); j++) {
        Map<String, String> map = (Map<String, String>) selectedTrees.get(j);
        for (int i = 0; i < selectedAreas.size(); i++) {
            sb.append("\n");
            //numbers
            double pd = 0;
            double maxpd = 0;
            int speciesFound = 0;
            int studySpecieCount = 1;
            try {
                //area pd
                pd = Double.parseDouble(areaPds.get(i).get(map.get(StringConstants.STUDY_ID)));
                //tree pd
                maxpd = Double.parseDouble(map.get("maxPd"));
                //species found in tree
                //Integer.parseInt();
                speciesFound = areaSpeciesMatches.get(i).get(map.get(StringConstants.STUDY_ID)).size();
                //tree species count
                studySpecieCount = Integer.parseInt(map.get("numberOfLeaves"));
            } catch (Exception e) {
            }
            //'current extent' does not have a map layer
            if (selectedAreas.get(i).getMapLayer() == null) {
                sb.append(toCSVString("Current extent")).append(",");
                sb.append(selectedAreas.get(i).getKm2Area()).append(",");
            } else {
                sb.append(toCSVString(selectedAreas.get(i).getMapLayer().getDisplayName())).append(",");
                sb.append(toCSVString(selectedAreas.get(i).getKm2Area())).append(",");
            }
            String s = areaPds.get(i).get(map.get(StringConstants.STUDY_ID));
            if (s == null) {
                s = "";
            }
            sb.append(s).append(",");
            sb.append(String.format("%.4f,", pd / maxpd));
            sb.append("" + speciesFound).append(",");
            sb.append(String.format("%.4f,", speciesFound / (double) studySpecieCount));
            //tree name
            sb.append(toCSVString(map.get("authors"))).append(",");
            //tree id
            sb.append(toCSVString(map.get("studyId"))).append(",");
            //doi
            sb.append(toCSVString(map.get("doi"))).append(",");
            //study name
            sb.append(toCSVString(map.get("studyName"))).append(",");
            //notes
            sb.append(toCSVString(map.get("notes"))).append(",");
            //tree pd
            sb.append(toCSVString(map.get("maxPd")));
        }
    }
    csv = sb.toString();
    try {
        csvCells = new CSVReader(new StringReader(csv)).readAll();
    } catch (Exception e) {
        LOGGER.error("failed to parse phylogenetic diversity list", e);
    }
}

Example 13 with CSVReader

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

the class UploadLayerListController method loadLayerList.

private void loadLayerList(Reader r) throws IOException {
    CSVReader reader = new CSVReader(r);
    //one line, read it
    StringBuilder sb = new StringBuilder();
    for (String s : reader.readNext()) {
        if (sb.length() > 0) {
            sb.append(",");
        }
        sb.append(s);
    }
    reader.close();
    if (callback != null) {
        try {
            callback.onEvent(new ForwardEvent("", this, null, sb.toString()));
        } catch (Exception e) {
            LOGGER.error("failed when calling ToolComposer callback", e);
        }
    }
}

Example 14 with CSVReader

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

the class InOutComposer method onFinish.

@Override
public boolean onFinish() {
    Query query = getSelectedSpecies();
    query = query.newFacet(new Facet("occurrence_status_s", "absent", false), false);
    if (query == null) {
        return false;
    }
    List<SelectedArea> sa = getSelectedAreas();
    //check the number of selected areas
    int countSelected = sa.size();
    if (autoCompleteLayerSelection != null && cAreasFromLayer.isChecked() && autoCompleteLayerAreas == null) {
        countSelected += 2;
    }
    if (countSelected != 2) {
        getMapComposer().showMessage(countSelected + " areas are selected. Select only 2 areas.");
        return false;
    }
    try {
        StringBuilder results = new StringBuilder();
        double inArea = 0;
        Query in;
        Query out;
        double outArea = 0;
        String outName;
        String inName;
        Map<String, String[]> onlyIn = new HashMap<String, String[]>();
        Map<String, String[]> onlyOut = new HashMap<String, String[]>();
        Map<String, String[]> both = new HashMap<String, String[]>();
        String[] speciesListHeader = null;
        //get area of the layer
        if (autoCompleteLayerSelection != null && cAreasFromLayer.isChecked() && autoCompleteLayerAreas == null) {
            // in/out for a selected layer and the marine/terrestrial complement
            String fieldId = CommonData.getLayerFacetNameDefault(autoCompleteLayerSelection);
            JSONParser jp = new JSONParser();
            JSONObject jo = (JSONObject) jp.parse(Util.readUrl(CommonData.getLayersServer() + "/field/" + fieldId));
            inName = "In area (" + jo.get("name") + ")";
            JSONArray objects = (JSONArray) jo.get("objects");
            for (int i = 0; i < objects.size(); i++) {
                if (((JSONObject) objects.get(i)).containsKey("area_km")) {
                    inArea += (Double) ((JSONObject) objects.get(i)).get("area_km");
                }
            }
            in = query.newFacet(new Facet(fieldId, "*", true), false);
            //determine complement area
            JSONObject fld = CommonData.getLayer(fieldId);
            JSONObject layer = (JSONObject) fld.get("layer");
            boolean isMarine = Util.isSameDomain(new String[] { "marine" }, Util.getDomain(layer));
            boolean isTerrestrial = Util.isSameDomain(new String[] { "terrestrial" }, Util.getDomain(layer));
            String terrestrialQuery = CommonData.getSettings().getProperty("in_out_report.terrestrial.query", "cl2013:*");
            String terrestrialName = CommonData.getSettings().getProperty("in_out_report.terrestrial.name", "Other - ASGS Australian States and Territories");
            Double terrestrialArea = Double.parseDouble(CommonData.getSettings().getProperty("in_out_report.terrestrial.area", "7719806.774"));
            String marineQuery = CommonData.getSettings().getProperty("in_out_report.marine.query", "cl21:*");
            String marineName = CommonData.getSettings().getProperty("in_out_report.marine.name", "Other - IMCRA 4");
            Double marineArea = Double.parseDouble(CommonData.getSettings().getProperty("in_out_report.marine.area", "8669607.781"));
            if (isMarine && isTerrestrial) {
                outName = marineName + " AND " + terrestrialName;
                outArea = terrestrialArea + marineArea;
                out = query.newFacets(Arrays.asList(new Facet[] { new Facet(fieldId, "*", false), Facet.parseFacet("(" + terrestrialQuery + " OR " + marineQuery + ")") }), false);
            } else if (isMarine) {
                outName = marineName;
                outArea = marineArea;
                out = query.newFacets(Arrays.asList(new Facet[] { new Facet(fieldId, "*", false), Facet.parseFacet(marineQuery) }), false);
            } else if (isTerrestrial) {
                outName = terrestrialName;
                outArea = terrestrialArea;
                out = query.newFacets(Arrays.asList(new Facet[] { new Facet(fieldId, "*", false), Facet.parseFacet(terrestrialQuery) }), false);
            } else {
                //world
                outName = "rest of the world";
                outArea = 510000000.0;
                out = query.newFacet(new Facet(fieldId, "*", false), false);
            }
            outArea -= inArea;
        } else {
            inName = sa.get(0).getMapLayer().getDisplayName();
            outName = sa.get(1).getMapLayer().getDisplayName();
            in = QueryUtil.queryFromSelectedArea(query, sa.get(0), false, null);
            out = QueryUtil.queryFromSelectedArea(query, sa.get(1), false, null);
            try {
                inArea = Double.parseDouble(sa.get(0).getKm2Area().replace(",", ""));
                outArea = Double.parseDouble(sa.get(1).getKm2Area().replace(",", ""));
            } catch (Exception e) {
            }
            //build species lists for comparison
            List<String[]> inSpeciesList = new CSVReader(new StringReader(in.speciesList())).readAll();
            List<String[]> outSpeciesList = new CSVReader(new StringReader(out.speciesList())).readAll();
            //used to exclude header
            int row = 0;
            for (String[] line : inSpeciesList) {
                if (row == 0) {
                    speciesListHeader = line;
                    row++;
                } else if (line.length > 0) {
                    onlyIn.put(line[0], line);
                }
            }
            row = 0;
            for (String[] line : outSpeciesList) {
                if (row == 0) {
                    //header will be missing if no species in inArea
                    speciesListHeader = line;
                    row++;
                } else if (line.length > 0) {
                    if (!onlyIn.containsKey(line[0])) {
                        onlyOut.put(line[0], line);
                    } else {
                        onlyIn.remove(line[0]);
                        both.put(line[0], line);
                    }
                }
            }
        }
        results.append("Species,Area name,Sq km,Occurrences,Species\n");
        results.append(getSelectedSpeciesName()).append(",");
        results.append(inName).append(",").append(inArea).append(",").append(in.getOccurrenceCount()).append(",").append(in.getSpeciesCount()).append("\n");
        results.append(getSelectedSpeciesName()).append(",");
        results.append(outName).append(" (").append(outName).append("),").append(outArea).append(",").append(out.getOccurrenceCount()).append(",").append(out.getSpeciesCount()).append("\n");
        if (onlyIn.size() + onlyOut.size() + both.size() > 0) {
            results.append("\n");
            results.append("\nSpecies found only in ").append(inName).append(",").append(String.format("%d", onlyIn.size()));
            results.append("\nSpecies found only in ").append(outName).append(",").append(String.format("%d", onlyOut.size()));
            results.append("\nSpecies found in both areas,").append(String.format("%d", both.size()));
            results.append("\n\n").append(StringUtils.join(speciesListHeader, ",", 0, speciesListHeader.length - 3)).append(",").append(inName).append(",").append(outName);
            for (String[] line : both.values()) {
                results.append("\n");
                for (int i = 0; i < line.length - 3; i++) results.append("\"").append(line[i].replace("\"", "\"\",")).append("\",");
                results.append("found,found");
            }
            for (String[] line : onlyIn.values()) {
                results.append("\n");
                for (int i = 0; i < line.length - 3; i++) results.append("\"").append(line[i].replace("\"", "\"\",")).append("\",");
                results.append("found,not found");
            }
            for (String[] line : onlyOut.values()) {
                results.append("\n");
                for (int i = 0; i < line.length - 3; i++) results.append("\"").append(line[i].replace("\"", "\"\",")).append("\",");
                results.append("not found,found");
            }
        }
        //show results
        String metadata = "<html><body>" + "<div class='aooeoo'>" + "<div>Report for: " + getSelectedSpeciesName() + "<br />" + inName + "<br />" + outName + "</div><br />" + "<table >" + "<tr><td>Area name</td><td>Sq km</td><td>Occurrences</td><td>Species</td></tr>" + "<tr><td>" + inName + "</td><td>" + String.format("%.2f", inArea) + "</td><td>" + in.getOccurrenceCount() + "</td><td>" + in.getSpeciesCount() + "</td></tr>" + "<tr><td>" + outName + "</td><td>" + String.format("%.2f", outArea) + "</td><td>" + out.getOccurrenceCount() + "</td><td>" + out.getSpeciesCount() + "</td></tr>";
        if (onlyIn.size() + onlyOut.size() + both.size() > 0) {
            metadata += "<tr><td>&nbsp;</td></tr>" + "<tr><td>Species found only in " + inName + "</td><td>" + String.format("%d", onlyIn.size()) + "</td></tr>" + "<tr><td>Species found only in " + outName + "</td><td>" + String.format("%d", onlyOut.size()) + "</td></tr>" + "<tr><td>Species found in both areas</td><td>" + String.format("%d", both.size()) + "</td></tr>";
        }
        metadata += "</table></div>";
        Event ev = new Event(StringConstants.ONCLICK, null, "Compare Areas Report\n" + metadata);
        getMapComposer().openHTML(ev);
        //download metadata as text
        Filedownload.save(results.toString(), "text/plain", "Compare Areas Report.csv");
        this.detach();
        return true;
    } catch (Exception e) {
        LOGGER.error("failed In Out finish", e);
    }
    return false;
}

Example 15 with CSVReader

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

the class ClassificationLegend method buildLegend.

void buildLegend() {
    try {
        StringBuilder slist = new StringBuilder();
        if (query != null) {
            if (StringConstants.GRID.equals(colourmode)) {
                slist.append("name,red,green,blue,count");
                for (int i = 0; i < 600; i += 100) {
                    slist.append(">");
                    slist.append("\n").append(i).append(",").append(LegendObject.getRGB(Legend.getLinearColour(i, 0, 500, 0xFFFFFF00, 0xFFFF0000))).append(",");
                }
            } else {
                slist.append(query.getLegend(colourmode).getTable());
            }
        } else {
            return;
        }
        try {
            legendLines = new CSVReader(new StringReader(slist.toString())).readAll();
            //reset selection when legendLines is rebuilt
            uncheckAll();
        } catch (IOException e) {
            LOGGER.error("failed to read legend list as csv", e);
        }
        legendLines.remove(0);
        String h = mapLayer.getHighlight();
        facet = Facet.parseFacet(h);
        divContinous.setVisible(false);
        //test for range (user upload)
        if (legendLines.size() > 1) {
            String first = legendLines.get(0)[0];
            if (first == null || first.length() == 0 || first.startsWith(StringConstants.UNKNOWN)) {
                first = legendLines.get(1)[0];
            }
            if (!checkmarks && query.getLegend(colourmode) != null && query.getLegend(colourmode).getNumericLegend() != null) {
                setupForNumericalList(h);
            //test for manual range (solr query)
            } else if (StringConstants.OCCURRENCE_YEAR.equals(colourmode)) {
                setupForBiocacheNumber(h, colourmode, true);
            } else if (StringConstants.OCCURRENCE_YEAR_DECADE.equals(colourmode) || StringConstants.DECADE.equals(colourmode)) {
                setupForBiocacheDecade();
            } else if (StringConstants.COORDINATE_UNCERTAINTY.equals(colourmode) || StringConstants.UNCERTAINTY.equals(colourmode)) {
                setupForBiocacheNumber(h, colourmode, false);
            } else if (StringConstants.MONTH.equals(colourmode)) {
                setupForBiocacheMonth();
            }
        }
        /* apply something to line onclick in lb */
        legend.setItemRenderer(new ListitemRenderer() {

            @Override
            public void render(Listitem li, Object data, int itemIdx) {
                String[] ss = (String[]) data;
                if (ss == null) {
                    return;
                }
                Checkbox cb = null;
                if (checkmarks) {
                    cb = new Checkbox();
                    cb.addEventListener("onCheck", new EventListener() {

                        @Override
                        public void onEvent(Event event) throws Exception {
                            String v = ((Listcell) event.getTarget().getParent().getParent().getChildren().get(1)).getLabel();
                            if (((CheckEvent) event).isChecked()) {
                                selectedList.add(v);
                            } else {
                                selectedList.remove(v);
                            }
                            lblSelectedCount.setValue(selectedList.size() + " selected");
                            if (selectedList.size() > 0) {
                                createInGroup.setVisible(true);
                                if (createOutGroup != null)
                                    createOutGroup.setVisible(true);
                                clearSelection.setVisible(true);
                            } else {
                                createInGroup.setVisible(false);
                                if (createOutGroup != null)
                                    createOutGroup.setVisible(false);
                                clearSelection.setVisible(false);
                            }
                            checkboxClick(event);
                        }
                    });
                    determineCheckboxState(cb, ss[0]);
                }
                Listcell lc;
                lc = new Listcell();
                if (cb != null) {
                    cb.setParent(lc);
                    //Do not display checkboxes for facets that are not simple
                    cb.setVisible(!disableselection && !ss[0].endsWith(" more"));
                }
                lc.setParent(li);
                if (readonly) {
                    lc = new Listcell(actualToDisplayLabel(ss[0]));
                } else {
                    lc = new Listcell("group " + ss[0]);
                }
                lc.setParent(li);
                int red = 0, green = 0, blue = 0;
                try {
                    red = Integer.parseInt(ss[1]);
                    green = Integer.parseInt(ss[2]);
                    blue = Integer.parseInt(ss[3]);
                } catch (Exception e) {
                    LOGGER.error("error parsing colours : " + ss[0], e);
                }
                lc = new Listcell("   ");
                lc.setStyle("background-color: rgb(" + red + "," + green + "," + blue + "); color: rgb(" + red + "," + green + "," + blue + ")");
                lc.setParent(li);
                //count
                try {
                    //don't display if it is not a number
                    Long.parseLong(ss[4]);
                    lhFourthColumn.setVisible(true);
                    lc = new Listcell(ss[4]);
                    lc.setParent(li);
                } catch (NumberFormatException e) {
                    lhFourthColumn.setVisible(false);
                    lhThirdColumn.setWidth("100%");
                    dCreateButtons.setVisible(!readonly);
                }
            }
        });
        legend.setModel(new SimpleListModel(legendLines));
        createInGroup.setVisible(!disableselection && mapLayer.getHighlight() != null && mapLayer.getHighlight().length() > 0);
        if (createOutGroup != null)
            createOutGroup.setVisible(!disableselection && mapLayer.getHighlight() != null && mapLayer.getHighlight().length() > 0);
        clearSelection.setVisible(!disableselection && mapLayer.getHighlight() != null && mapLayer.getHighlight().length() > 0);
        if (divContinous.isVisible()) {
            int[] state = getState();
            if (state[0] > 1) {
                setEnableContinousControls(false);
            } else {
                updateD();
            }
            getFellow("txtSearch").setVisible(false);
        } else {
            getFellow("txtSearch").setVisible(true);
        }
    } catch (Exception e) {
        LOGGER.error("error building classification legend, pid: " + pid, e);
    }
}