Examples with Query au.org.ala.spatial.util.Query used on opensource projects

Example 6 with Query

use of au.org.ala.spatial.util.Query in project spatial-portal by AtlasOfLivingAustralia.

the class SamplingComposer method fixFocus.

@Override
void fixFocus() {
    switch(currentStep) {
        case 1:
            rgArea.setFocus(true);
            break;
        case 2:
            if (rSpeciesSearch.isChecked()) {
                searchSpeciesACComp.getAutoComplete().setFocus(true);
            } else {
                rgSpecies.setFocus(true);
            }
            break;
        case 3:
            lbListLayers.setFocus(true);
            // tick and disable all 'DEFAULT' sampled layers
            if (getSelectedSpecies() != null) {
                Query q = getSelectedSpecies();
                String[] defaultFields = q.getDefaultDownloadFields();
                if (defaultFields.length > 0) {
                    lbListLayers.selectLayersAndDisable(defaultFields);
                }
            }
            updateLayerSelectionCount();
            break;
        default:
            LOGGER.error("invalid step for SamplingComposer: " + currentStep);
    }
}

Example 7 with Query

use of au.org.ala.spatial.util.Query in project spatial-portal by AtlasOfLivingAustralia.

the class SamplingComposer method download.

public boolean download(Event event) {
    try {
        SelectedArea sa = getSelectedArea();
        Query query = QueryUtil.queryFromSelectedArea(getSelectedSpecies(), sa, false, getGeospatialKosher());
        // test size
        if (query.getOccurrenceCount() <= 0) {
            getMapComposer().showMessage("No occurrences selected. Please try again", this);
            return false;
        }
        // translate layer names
        String[] layers = null;
        String[] layersDisplaynames = null;
        String envlayers = getSelectedLayersWithDisplayNames();
        if (envlayers.length() > 0) {
            layers = envlayers.split(":");
            layersDisplaynames = new String[layers.length];
            for (int i = 0; i < layers.length; i++) {
                String[] l = layers[i].split("\\|");
                String newName = CommonData.getLayerFacetName(l[0]);
                layers[i] = newName;
                layersDisplaynames[i] = l[1];
            }
        }
        if (query instanceof BiocacheQuery) {
            String[] inBiocache = null;
            String[] outBiocache;
            String[] outBiocacheDN;
            // split layers into 'in biocache' and 'out of biocache'
            Set<String> biocacheLayers = CommonData.getBiocacheLayerList();
            List<String> aInBiocache = new ArrayList<String>();
            List<String> aOutBiocache = new ArrayList<String>();
            List<String> aInBiocacheDN = new ArrayList<String>();
            List<String> aOutBiocacheDN = new ArrayList<String>();
            if (layers != null) {
                for (int i = 0; i < layers.length; i++) {
                    String s = layers[i];
                    if (biocacheLayers.contains(s)) {
                        aInBiocache.add(s);
                        aInBiocacheDN.add(layersDisplaynames[i]);
                    } else {
                        aOutBiocache.add(s);
                        aOutBiocacheDN.add(layersDisplaynames[i]);
                    }
                }
            }
            if (!aInBiocache.isEmpty()) {
                inBiocache = new String[aInBiocache.size()];
                aInBiocache.toArray(inBiocache);
            }
            if (!aOutBiocache.isEmpty()) {
                outBiocache = new String[aOutBiocache.size()];
                aOutBiocache.toArray(outBiocache);
                outBiocacheDN = new String[aOutBiocacheDN.size()];
                aOutBiocacheDN.toArray(outBiocacheDN);
                getMapComposer().setDownloadSecondQuery(query);
                getMapComposer().setDownloadSecondLayers(outBiocache, outBiocacheDN);
                SamplingAnalysisDownloadController c = (SamplingAnalysisDownloadController) Executions.createComponents("/WEB-INF/zul/output/SamplingAnalysisDownload.zul", getMapComposer(), null);
                c.setParent(getMapComposer());
                c.doModal();
            } else {
                getMapComposer().setDownloadSecondQuery(null);
                getMapComposer().setDownloadSecondLayers(null, null);
            }
            // test for URL download
            String url = query.getDownloadUrl(inBiocache);
            LOGGER.debug("Sending file to user: " + url);
            Events.echoEvent(StringConstants.OPEN_HTML, getMapComposer(), "Download\n" + url);
            try {
                remoteLogger.logMapAnalysis("species sampling", "Export - Species Sampling", sa.getWkt(), query.getName(), envlayers, pid, "", "download");
            } catch (Exception e) {
                LOGGER.error("remote logger error", e);
            }
            this.detach();
        } else {
            String fileUrl = query.getDownloadUrl(layers);
            Filedownload.save(new URL(fileUrl).openStream(), "application/zip", query.getName().replaceAll(" ", "_") + "_sample_" + ".zip");
            try {
                remoteLogger.logMapAnalysis("species sampling", "Export - Species Sampling", sa.getWkt(), query.getName(), envlayers, pid, "", "");
            } catch (Exception e) {
                LOGGER.error("remote logger error", e);
            }
            this.detach();
        }
        return true;
    } catch (Exception e) {
        LOGGER.error("Exception calling sampling.download:", e);
        getMapComposer().showMessage("Unknown error.", this);
    }
    return false;
}

Example 8 with Query

use of au.org.ala.spatial.util.Query in project spatial-portal by AtlasOfLivingAustralia.

the class MetadataEvent method onEvent.

@Override
public void onEvent(Event event) throws Exception {
    MapComposer mc = (MapComposer) event.getPage().getFellow(StringConstants.MAPPORTALPAGE);
    MapLayer mapLayer = mc.getMapLayer(layerName);
    if (mapLayer != null) {
        if (mapLayer.getSpeciesQuery() != null) {
            // TODO: update for scatterplot layers
            Query q = mapLayer.getSpeciesQuery();
            Events.echoEvent(StringConstants.OPEN_HTML, mc, q.getMetadataHtml());
        } else if (mapLayer.getMapLayerMetadata().getMoreInfo() != null && mapLayer.getMapLayerMetadata().getMoreInfo().startsWith("http://")) {
            String infourl = mapLayer.getMapLayerMetadata().getMoreInfo().replace("__", ".");
            if (mapLayer.getSubType() == LayerUtilitiesImpl.SCATTERPLOT) {
                ScatterplotDataDTO data = mapLayer.getScatterplotDataDTO();
                infourl += "?dparam=X-Layer:" + data.getLayer1Name();
                infourl += "&dparam=Y-Layer:" + data.getLayer2Name();
            }
            // send the user to the BIE page for the species
            Events.echoEvent(StringConstants.OPEN_URL, mc, infourl);
        } else if (mapLayer.getMapLayerMetadata().getMoreInfo() != null && mapLayer.getMapLayerMetadata().getMoreInfo().length() > 0) {
            Events.echoEvent(StringConstants.OPEN_HTML, mc, mapLayer.getMapLayerMetadata().getMoreInfo());
        } else {
            mc.showMessage("Metadata currently unavailable");
        }
    }
}

Example 9 with Query

use of au.org.ala.spatial.util.Query 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 10 with Query

use of au.org.ala.spatial.util.Query in project spatial-portal by AtlasOfLivingAustralia.

the class OpenLayersJavascriptImpl method defineWMSMapLayer.

/**
 * create an instance of OpenLayers.Layer.WMS.
 * <p/>
 * Base layers will be rendered differently and stored in the baseLayers
 * associative array instead of the mapLayers associative array
 *
 * @param layer
 * @return
 */
public String defineWMSMapLayer(MapLayer layer) {
    String associativeArray;
    String gutter = "0";
    String params = "";
    if (layer.isBaseLayer()) {
        associativeArray = StringConstants.BASE_LAYERS;
    } else {
        associativeArray = StringConstants.MAP_LAYERS;
    }
    if (!Validate.empty(layer.getCql())) {
        params = "CQL_FILTER: '" + layer.getCqlJS() + "' ";
        params += ", ";
    }
    if (!Validate.empty(layer.getEnvParams())) {
        try {
            params += "env: '" + URLEncoder.encode(layer.getEnvParams(), StringConstants.UTF_8) + "', ";
        } catch (UnsupportedEncodingException e) {
            LOGGER.error("failed to encode env params : " + layer.getEnvParams().replace("'", "\\'"), e);
        }
    }
    String dynamicStyle = "";
    if (layer.isPolygonLayer()) {
        String colour = Integer.toHexString((0xFF0000 & (layer.getRedVal() << 16)) | (0x00FF00 & layer.getGreenVal() << 8) | (0x0000FF & layer.getBlueVal()));
        while (colour.length() < 6) {
            colour = "0" + colour;
        }
        String filter;
        /*
                two types of areas are displayed as WMS.
                1. environmental envelopes. these are backed by a grid file.
                2. layerdb, objects table, areas referenced by a pid.  these are geometries.
             */
        if (layer.getUri().contains("ALA:envelope")) {
            filter = "";
            if (!layer.getUri().contains("sld_body")) {
                filter = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><StyledLayerDescriptor xmlns=\"http://www.opengis.net/sld\">" + "<NamedLayer><Name>" + layerUtilities.getLayer(layer.getUri()) + "</Name>" + "<UserStyle><FeatureTypeStyle><Rule><RasterSymbolizer><Geometry></Geometry>" + "<ColorMap>" + "<ColorMapEntry color=\"#ffffff\" opacity=\"0\" quantity=\"0\"/>" + "<ColorMapEntry color=\"#" + colour + "\" opacity=\"1\" quantity=\"1\" />" + "</ColorMap></RasterSymbolizer></Rule></FeatureTypeStyle></UserStyle></NamedLayer></StyledLayerDescriptor>";
            }
        } else if (layer.getUri() != null && layer.getUri().contains("ColorMapEntry")) {
            // area from grid as contextual layer
            String uri = layer.getUri();
            // replace with current colour
            String str = "ColorMapEntry+color%3D%220x";
            int p = uri.indexOf(str);
            while (p > 0 && p + str.length() + 6 < uri.length()) {
                uri = uri.substring(0, p + str.length()) + colour + uri.substring(p + str.length() + 6);
                p = uri.indexOf(str, p + 1);
            }
            layer.setUri(uri);
            filter = "";
        } else {
            filter = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><StyledLayerDescriptor version=\"1.0.0\" xmlns=\"http://www.opengis.net/sld\">" + "<NamedLayer><Name>" + layerUtilities.getLayer(layer.getUri()) + "</Name>" + "<UserStyle><FeatureTypeStyle><Rule><Title>Polygon</Title><PolygonSymbolizer><Fill>" + "<CssParameter name=\"fill\">#" + colour + "</CssParameter></Fill>" + "</PolygonSymbolizer></Rule></FeatureTypeStyle></UserStyle></NamedLayer></StyledLayerDescriptor>";
        }
        try {
            if (filter.length() == 0) {
                dynamicStyle = "";
            } else {
                dynamicStyle = "&sld_body=" + URLEncoder.encode(filter, StringConstants.UTF_8);
            }
        } catch (Exception e) {
            LOGGER.debug("invalid filter sld", e);
        }
    }
    String script = " " + associativeArray + "['" + layer.getUniqueIdJS() + "'] = new OpenLayers.Layer.WMS(" + "  '" + layer.getNameJS() + "', " + "  '" + layer.getUriJS().replace("wms?service=WMS&version=1.1.0&request=GetMap&", "wms\\/reflect?") + dynamicStyle + "', " + "  {" + ((StringConstants.DEFAULT.equals(layer.getSelectedStyleNameJS())) ? "" : "   styles: '" + layer.getSelectedStyleNameJS() + "', ") + "   layers: '" + layer.getLayerJS() + "', " + "   format: '" + layer.getImageFormat() + "', " + "         srs: 'epsg:3857', " + "   transparent: " + (!layer.isBaseLayer()) + ", " + "   " + params + wmsVersionDeclaration(layer) + "  }, " + "  { " + "   isBaseLayer: " + layer.isBaseLayer() + ", " + "   opacity: " + layer.getOpacity() + ", " + "   queryable: true, " + "   gutter: " + gutter + ", " + "   wrapDateLine: true, displayname: '" + StringEscapeUtils.escapeJavaScript(layer.getDisplayName()) + "'" + "  }  " + " ); " + // tiles around the viewport!!
    associativeArray + "['" + layer.getUniqueIdJS() + "']" + ".getFeatureInfoBuffer =" + CommonData.getSettings().getProperty("get_feature_info_buffer") + "; ";
    // add ws and bs urls for species layers
    if (layer.getSpeciesQuery() != null) {
        Query q = layer.getSpeciesQuery();
        if (q instanceof BiocacheQuery) {
            BiocacheQuery bq = (BiocacheQuery) q;
            try {
                script += associativeArray + "['" + layer.getUniqueIdJS() + "']" + ".ws ='" + StringEscapeUtils.escapeJavaScript(bq.getWS()) + "'; " + associativeArray + "['" + layer.getUniqueIdJS() + "']" + ".bs ='" + StringEscapeUtils.escapeJavaScript(bq.getBS()) + "'; ";
            } catch (Exception e) {
                LOGGER.error("error escaping for JS: " + bq.getBS(), e);
            }
        }
        if (q.flagRecordCount() > 0) {
            script += "parent.addFlaggedRecords('" + layer.getNameJS() + "','" + StringEscapeUtils.escapeJavaScript(q.getFlaggedRecords()) + "'); ";
        }
    }
    if (!layer.isBaseLayer()) {
        script += " " + associativeArray + "['" + layer.getUniqueIdJS() + "']" + ".featureInfoResponseType=" + layer.getType() + "; ";
    }
    // register for loading images...
    script += "registerLayer(" + associativeArray + "['" + layer.getUniqueIdJS() + "']);";
    return wrapWithSafeToProceed(script);
}