Examples with LabeledCSVParser com.Ostermiller.util.LabeledCSVParser used on opensource projects

Example 51 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForWrast method createLocationMap.

private void createLocationMap() throws StudyImporterException {
    Map<String, List<LatLng>> locations = new HashMap<String, List<LatLng>>();
    LabeledCSVParser parser = null;
    try {
        parser = parserFactory.createParser(LAVACA_BAY_LOCATIONS, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String habitateDef = parser.getValueByLabel(COLUMN_MAPPER.get(HABITAT));
            String regionDef = parser.getValueByLabel(COLUMN_MAPPER.get(REGION));
            String siteDef = parser.getValueByLabel(COLUMN_MAPPER.get(SITE));
            String latitude = parser.getValueByLabel("Latitude");
            if (null == latitude) {
                throw new StudyImporterException(createMsgPrefix(parser) + " missing latitude");
            }
            String longitude = parser.getValueByLabel("Longitude");
            if (null == longitude) {
                throw new StudyImporterException(createMsgPrefix(parser) + " missing longitude");
            }
            Double lat;
            try {
                lat = Double.parseDouble(latitude);
            } catch (NumberFormatException ex) {
                throw new StudyImporterException(createMsgPrefix(parser) + " invalid latitude [" + latitude + "]");
            }
            Double lng;
            try {
                lng = Double.parseDouble(longitude);
            } catch (NumberFormatException ex) {
                throw new StudyImporterException("in [" + LAVACA_BAY_LOCATIONS + ":" + parser.getLastLineNumber() + "]: invalid longtude [" + longitude + "]");
            }
            LatLng latLng = new LatLng(lat, lng);
            String locationId = createLocationId(habitateDef, regionDef, siteDef);
            List<LatLng> latLngs = locations.get(locationId);
            if (null == latLngs) {
                latLngs = new ArrayList<LatLng>();
                locations.put(locationId, latLngs);
            }
            latLngs.add(latLng);
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem to reading from [" + LAVACA_BAY_LOCATIONS + "]", e);
    }
    locationMap = new HashMap<String, LatLng>();
    for (Map.Entry<String, List<LatLng>> entry : locations.entrySet()) {
        Double lat = 0.0d;
        Double lng = 0.0d;
        int count = 0;
        for (LatLng latLng : entry.getValue()) {
            lat += latLng.getLat();
            lng += latLng.getLng();
            count++;
        }
        if (count == 0) {
            throw new StudyImporterException("must have more than one location per locationId");
        }
        locationMap.put(entry.getKey(), new LatLng(lat / count, lng / count));
    }
}

Example 52 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForStrona method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    try {
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl("strona2013", SOURCE + " . " + CitationUtil.createLastAccessedString(RESOURCE_PATH), "http://dx.doi.org/10.1890/12-1419.1", SOURCE));
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                try {
                    String parasiteName = StringUtils.trim(dataParser.getValueByLabel("P_SP"));
                    String hostName = StringUtils.trim(dataParser.getValueByLabel("H_SP"));
                    if (areNamesAvailable(parasiteName, hostName)) {
                        Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                        Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                        parasite.interactsWith(host, InteractType.PARASITE_OF);
                    }
                } catch (NodeFactoryException | NumberFormatException e) {
                    throw new StudyImporterException("failed to import line [" + (dataParser.lastLineNumber() + 1) + "]", e);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("problem importing [" + RESOURCE_PATH + "]", e);
    }
}

Example 53 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForSimons method importStudy.

private Study importStudy(ParserFactory parserFactory, String studyResource) throws StudyImporterException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Simons 1997", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, ExternalIdUtil.toCitation("James D. Simons", "Food habits and trophic structure of the demersal fish assemblages on the Mississippi-Alabama continental shelf.", "1997")));
    try {
        LabeledCSVParser csvParser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        Map<String, String> columnMapper = COLUMN_MAPPER;
        LengthParser parser = new LengthRangeParserImpl(columnMapper.get(LENGTH_RANGE_IN_MM));
        while (csvParser.getLine() != null) {
            addNextRecordToStudy(csvParser, study, COLUMN_MAPPER, parser);
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to createTaxon study [" + studyResource + "]", e);
    }
    return study;
}

Example 54 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForWebOfLife method importNetwork.

public void importNetwork(InteractType interactType1, Location networkLocation, Study study, File file) throws IOException, NodeFactoryException {
    LabeledCSVParser interactions = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(file));
    final String[] targetLabels = interactions.getLabels();
    List<String> targetTaxonNames = new ArrayList<String>();
    List<String> ignoredLabels = Arrays.asList("number of hosts sampled", "");
    for (String targetLabel : targetLabels) {
        String trimmedLabel = StringUtils.trim(targetLabel);
        if (StringUtils.isNotBlank(targetLabel) || !ignoredLabels.contains(trimmedLabel)) {
            targetTaxonNames.add(targetLabel);
        }
    }
    String[] line;
    while ((line = interactions.getLine()) != null) {
        String sourceTaxonName = line[0];
        final Specimen sourceSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(sourceTaxonName, null));
        sourceSpecimen.caughtIn(networkLocation);
        for (String targetTaxonName : targetTaxonNames) {
            final String valueByLabel = StringUtils.trim(interactions.getValueByLabel(targetTaxonName));
            if (StringUtils.isNotBlank(valueByLabel) && !StringUtils.equals("0", valueByLabel)) {
                final Specimen targetSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(targetTaxonName, null));
                targetSpecimen.caughtIn(networkLocation);
                sourceSpecimen.interactsWith(targetSpecimen, interactType1);
            }
        }
    }
}

Example 55 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForSIAD method downloadAndImportResource.

private void downloadAndImportResource(String resource, String source) throws StudyImporterException {
    try {
        LabeledCSVParser labeledCSVParser = parserFactory.createParser(resource, "UTF-8");
        labeledCSVParser.changeDelimiter('\t');
        while (labeledCSVParser.getLine() != null) {
            String name = labeledCSVParser.getValueByLabel("name");
            String ref = labeledCSVParser.getValueByLabel("source");
            String title = "SIAD-" + ref;
            String citation = "ABRS 2009. Australian Faunal Directory. " + name + ". Australian Biological Resources StudyNode, Canberra. " + CitationUtil.createLastAccessedString(ref);
            StudyImpl study1 = new StudyImpl(title, source, null, citation);
            study1.setExternalId(ref);
            Study study = nodeFactory.getOrCreateStudy(study1);
            Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(name, null));
            String hostName = labeledCSVParser.getValueByLabel("host name");
            Specimen hostSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
            InteractType type = map.get(labeledCSVParser.getValueByLabel("interaction"));
            specimen.interactsWith(hostSpecimen, type);
        }
    } catch (FileNotFoundException e) {
        throw new StudyImporterException("failed to open tmp file", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to map data", e);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + resource + "]", e);
    }
}