Examples with LocationImpl org.eol.globi.domain.LocationImpl used on opensource projects

Example 11 with LocationImpl

use of org.eol.globi.domain.LocationImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForICES method parseLocation.

private Location parseLocation(LabeledCSVParser parser) throws StudyImporterException {
    Double lat = parseDoubleField(parser, "Latitude");
    Double lon = parseDoubleField(parser, "Longitude");
    Double depth = parseDoubleField(parser, "Depth");
    try {
        return nodeFactory.getOrCreateLocation(new LocationImpl(lat, lon, depth == null ? null : -depth, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
}

Example 12 with LocationImpl

use of org.eol.globi.domain.LocationImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForHechinger method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study = createStudy();
    try {
        LabeledCSVParser nodes = parserFactory.createParser(getNodesResourceName(), CharsetConstant.UTF8);
        nodes.changeDelimiter(getDelimiter());
        Map<Integer, Term> stageForNode = new HashMap<>();
        Map<Integer, String> taxonForNode = new HashMap<Integer, String>();
        while (nodes.getLine() != null) {
            Integer nodeId = getNodeId(nodes);
            if (nodeId != null) {
                String name = parseMostGranularTaxonName(nodes);
                if (StringUtils.isBlank(name)) {
                    name = nodes.getValueByLabel("WorkingName");
                    if (StringUtils.isBlank(name)) {
                        getLogger().warn(study, "failed to find name for node on line [" + nodes.lastLineNumber() + "]");
                    }
                }
                if (StringUtils.isNotBlank(name)) {
                    try {
                        taxonForNode.put(nodeId, name);
                        String stage = nodes.getValueByLabel("Stage");
                        stageForNode.put(nodeId, nodeFactory.getOrCreateLifeStage(getNamespace() + ":" + stage, stage));
                    } catch (NodeFactoryException e) {
                        throw new StudyImporterException("failed to reader line [" + nodes.lastLineNumber() + "]", e);
                    }
                }
            }
        }
        LabeledCSVParser links = parserFactory.createParser(getLinksResourceName(), CharsetConstant.UTF8);
        links.changeDelimiter(getDelimiter());
        while (links.getLine() != null) {
            List<Location> locations = new ArrayList<>();
            if (getLocation() != null) {
                Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(getLocation().getLat(), getLocation().getLng(), null, null));
                if (loc != null) {
                    locations.add(loc);
                }
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtCSM"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(34.403511, -119.537873, null, null)));
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtEPB"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(31.748606, -116.626854, null, null)));
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtBSQ"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(30.378207, -115.938835, null, null)));
            }
            for (Location location : locations) {
                addLink(study, stageForNode, taxonForNode, links, location);
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed import study", e);
    }
}

Example 13 with LocationImpl

use of org.eol.globi.domain.LocationImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForGoMexSI2 method parseLocation.

protected static Location parseLocation(String locationResource, LabeledCSVParser parser) throws StudyImporterException {
    Double latitude = getMandatoryDoubleValue(locationResource, parser, "LOC_CENTR_LAT");
    Double longitude = getMandatoryDoubleValue(locationResource, parser, "LOC_CENTR_LONG");
    Double depth = getMandatoryDoubleValue(locationResource, parser, "MN_DEP_SAMP");
    final String polyCoords = parser.getValueByLabel("LOC_POLY_COORDS");
    String footprintWKT = polyCoordsToWKT(polyCoords);
    final LocationImpl location = new LocationImpl(latitude, longitude, depth == null ? null : -depth, StringUtils.isBlank(footprintWKT) ? null : StringUtils.trim(footprintWKT));
    final String locality = parser.getValueByLabel("LOCALE_NAME");
    if (StringUtils.isNotBlank(locality)) {
        location.setLocality(locality);
    }
    return location;
}

Example 14 with LocationImpl

use of org.eol.globi.domain.LocationImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForBarnesTest method importHeadAndTail.

@Test
public void importHeadAndTail() throws IOException, NodeFactoryException, StudyImporterException {
    final String firstFourLines = "Record number\tIn-ref ID\tIndividual ID\tPredator\tPredator common name\tPredator  taxon\tPredator lifestage\tType of feeding interaction\tPredator length\tPredator length unit\tPredator dimension measured\tPredator standard length\tPredator fork length\tPredator total length\tPredator TL/FL/SL conversion reference\tStandardised predator length\tPredator measurement type\tPredator length-mass conversion method\tPredator length-mass conversion reference\tPredator quality of length-mass conversion\tPredator mass\tPredator mass unit\tPredator mass check\tPredator mass check diff\tPredator ratio mass/mass\tSI predator mass\tDiet coverage\tPrey\tPrey common name\tPrey taxon\tPrey length\tPrey length unit\tPrey conversion to length method\tPrey quality of conversion to length\tPrey conversion to length reference\tSI prey length\tPrey dimension measured\tPrey width\tPrey width unit\tPrey measurement type\tPrey mass\tPrey mass unit\tPrey mass check\tPrey mass check diff\tPrey ratio mass/mass\tSI prey mass\tPrey conversion to mass method\tPrey conversion to mass reference\tPrey quality of conversion to mass\tGeographic location\tLatitude\tLongitude\tDepth\tMean annual temp\tSD annual temp\tMean PP\tSD PP\tReference\tSpecific habitat\tNotes / assumptions\n" + "1\tATSH063\t1\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t7.8000E+02\tmm\tfork length\t7.5433E+02\t7.8000E+02\t9.3990E+02\tFishbase (species)\t9.3990E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t1.5399E+03\tg\t4.3453E+04\t4.1913E+04\t2.8218E+01\t1.5399E+03\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t1.1259E+02\tmm\tn/a\t0\tn/a\t1.1259E+01\tlength\tn/a\tn/a\tindividual\t1.4274E+01\tg\t7.4699E+01\t6.0425E+01\t5.2333E+00\t1.4274E+01\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "2\tATSH080\t2\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t7.9000E+02\tmm\tfork length\t7.6400E+02\t7.9000E+02\t9.5195E+02\tFishbase (species)\t9.5195E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t1.5978E+03\tg\t4.5146E+04\t4.3548E+04\t2.8256E+01\t1.5978E+03\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t8.4443E+01\tmm\tn/a\t0\tn/a\t8.4443E+00\tlength\tn/a\tn/a\tindividual\t6.0213E+00\tg\t3.1511E+01\t2.5490E+01\t5.2333E+00\t6.0213E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "3\tATSH089\t3\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t8.3000E+02\tmm\tfork length\t8.0269E+02\t8.3000E+02\t1.0002E+03\tFishbase (species)\t1.0002E+02\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t1.8436E+03\tg\t5.2357E+04\t5.0513E+04\t2.8400E+01\t1.8436E+03\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t1.0595E+02\tmm\tn/a\t0\tn/a\t1.0595E+01\tlength\tn/a\tn/a\tindividual\t1.1893E+01\tg\t6.2242E+01\t5.0349E+01\t5.2333E+00\t1.1893E+01\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "4\tATSH143\t4\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.9000E+02\tmm\tfork length\t2.8046E+02\t2.9000E+02\t3.4945E+02\tFishbase (species)\t3.4945E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t8.7631E+01\tg\t2.2332E+03\t2.1456E+03\t2.5484E+01\t8.7631E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t9.3301E+01\tmm\tn/a\t0\tn/a\t9.3301E+00\tlength\tn/a\tn/a\tindividual\t8.1220E+00\tg\t4.2505E+01\t3.4383E+01\t5.2333E+00\t8.1220E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "5\tATSH161\t5\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.6000E+02\tmm\tfork length\t2.5144E+02\t2.6000E+02\t3.1330E+02\tFishbase (species)\t3.1330E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t6.3866E+01\tg\t1.6094E+03\t1.5455E+03\t2.5199E+01\t6.3866E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t8.6900E+01\tmm\tn/a\t0\tn/a\t8.6900E+00\tlength\tn/a\tn/a\tindividual\t6.5623E+00\tg\t3.4343E+01\t2.7780E+01\t5.2333E+00\t6.5623E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "6\tATSH166\t6\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.8000E+02\tmm\tfork length\t2.7079E+02\t2.8000E+02\t3.3740E+02\tFishbase (species)\t3.3740E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t7.9161E+01\tg\t2.0101E+03\t1.9309E+03\t2.5392E+01\t7.9161E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t8.1465E+01\tmm\tn/a\t0\tn/a\t8.1465E+00\tlength\tn/a\tn/a\tindividual\t5.4065E+00\tg\t2.8294E+01\t2.2888E+01\t5.2333E+00\t5.4065E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "7\tATSH172\t7\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.7000E+02\tmm\tfork length\t2.6112E+02\t2.7000E+02\t3.2535E+02\tFishbase (species)\t3.2535E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t7.1245E+01\tg\t1.8023E+03\t1.7311E+03\t2.5298E+01\t7.1245E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t7.6371E+01\tmm\tn/a\t0\tn/a\t7.6371E+00\tlength\tn/a\tn/a\tindividual\t4.4543E+00\tg\t2.3311E+01\t1.8857E+01\t5.2333E+00\t4.4543E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "8\tATSH192\t8\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.9500E+02\tmm\tfork length\t2.8529E+02\t2.9500E+02\t3.5548E+02\tFishbase (species)\t3.5548E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t9.2080E+01\tg\t2.3507E+03\t2.2587E+03\t2.5529E+01\t9.2080E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t8.4262E+01\tmm\tn/a\t0\tn/a\t8.4262E+00\tlength\tn/a\tn/a\tindividual\t5.9828E+00\tg\t3.1310E+01\t2.5327E+01\t5.2333E+00\t5.9828E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "9\tATSH205\t9\tRhizoprionodon terraenovae\tAtlantic sharpnose shark\tectotherm vertebrate\tadult\tpredacious/piscivorous\t2.8000E+02\tmm\tfork length\t2.7079E+02\t2.8000E+02\t3.3740E+02\tFishbase (species)\t3.3740E+01\tindividual\tM=0.0056SL^2.897 \tBonfil et al. (1990)\t1\t7.9161E+01\tg\t2.0101E+03\t1.9309E+03\t2.5392E+01\t7.9161E+01\tall\tteleosts/molluscs/crustaceans\tteleosts/molluscs/crustaceans\tmixed\t8.8580E+01\tmm\tn/a\t0\tn/a\t8.8580E+00\tlength\tn/a\tn/a\tindividual\t6.9504E+00\tg\t3.6374E+01\t2.9423E+01\t5.2333E+00\t6.9504E+00\tM=0.01L^3\tGeneralised\t5\t\"Apalachicola Bay, Florida\"\t29�40'N\t85�10'W\t30\t24.1\t4.2\t866\t214\tBethea et al (2004)\tCoastal Bay\tNone\n" + "34922\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t4.2580E+02\tmm\ttotal length\t3.4916E+02\t0.0000E+00\t4.2580E+02\tFishbase (species)\t4.2580E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t7.1462E+02\tg\t4.0401E+03\t3.3255E+03\t5.6535E+00\t7.1462E+02\tall\tDeltentosteus quadrimaculatus\tFour-spotted goby\tectotherm vertebrate\t6.9190E+00\tcm\tL = 10^ ((logM-log(0.0074))/3.05)\t1\tMerella et al. (1997)\t6.9190E+00\tmass\tn/a\tn/a\tindividual\t2.7000E+00\tg\t1.7334E+01\t1.4634E+01\t6.4201E+00\t2.7000E+00\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34923\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t1.1920E+02\tmm\ttotal length\t9.7744E+01\t0.0000E+00\t1.1920E+02\tFishbase (species)\t1.1920E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t1.7550E+01\tg\t8.8635E+01\t7.1085E+01\t5.0505E+00\t1.7550E+01\tall\tLepidotrigla cavillone\tLarge-scaled gurnard\tectotherm vertebrate\t4.4221E+00\tcm\tL = 10^ ((logM-log(0.0078))/3.194)\t1\tPapaconstantinou (1982)\t4.4221E+00\tmass\tn/a\tn/a\tindividual\t9.0000E-01\tg\t4.5256E+00\t3.6256E+00\t5.0284E+00\t9.0000E-01\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34924\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t1.5410E+02\tmm\ttotal length\t1.2636E+02\t0.0000E+00\t1.5410E+02\tFishbase (species)\t1.5410E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t3.7066E+01\tg\t1.9151E+02\t1.5444E+02\t5.1667E+00\t3.7066E+01\tall\tLepidotrigla cavillone\tLarge-scaled gurnard\tectotherm vertebrate\t3.6788E+00\tcm\tL = 10^ ((logM-log(0.0078))/3.194)\t1\tPapaconstantinou (1982)\t3.6788E+00\tmass\tn/a\tn/a\tindividual\t5.0000E-01\tg\t2.6056E+00\t2.1056E+00\t5.2112E+00\t5.0000E-01\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34925\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t3.5470E+02\tmm\ttotal length\t2.9085E+02\t0.0000E+00\t3.5470E+02\tFishbase (species)\t3.5470E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t4.1983E+02\tg\t2.3354E+03\t1.9156E+03\t5.5628E+00\t4.1983E+02\tall\tTrachurus sp.\tfish\tectotherm vertebrate\t2.4112E+01\tcm\tL = 10^ ((logM-log(0.0072))/3.0327)\t2\tDorel (1986)\t2.4112E+01\tmass\tn/a\tn/a\tindividual\t1.1200E+02\tg\t7.3361E+02\t6.2161E+02\t6.5501E+00\t1.1200E+02\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34926\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t2.6470E+02\tmm\ttotal length\t2.1705E+02\t0.0000E+00\t2.6470E+02\tFishbase (species)\t2.6470E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t1.7907E+02\tg\t9.7060E+02\t7.9153E+02\t5.4204E+00\t1.7907E+02\tall\tGaidropsarus sp.\trockling\tectotherm vertebrate\t1.0897E+01\tcm\tL = 10^ ((logM-log(0.0053))/3.0262)\t2\tFroese & Pauly (2007)\t1.0897E+01\tmass\tn/a\tn/a\tindividual\t7.3000E+00\tg\t6.7709E+01\t6.0409E+01\t9.2752E+00\t7.3000E+00\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34927\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t3.7980E+02\tmm\ttotal length\t3.1144E+02\t0.0000E+00\t3.7980E+02\tFishbase (species)\t3.7980E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t5.1230E+02\tg\t2.8671E+03\t2.3548E+03\t5.5966E+00\t5.1230E+02\tall\tGaidropsarus sp.\trockling\tectotherm vertebrate\t6.5987E+00\tcm\tL = 10^ ((logM-log(0.0053))/3.0262)\t2\tFroese & Pauly (2007)\t6.5987E+00\tmass\tn/a\tn/a\tindividual\t1.6000E+00\tg\t1.5037E+01\t1.3437E+01\t9.3979E+00\t1.6000E+00\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34928\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t3.7980E+02\tmm\ttotal length\t3.1144E+02\t0.0000E+00\t3.7980E+02\tFishbase (species)\t3.7980E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t5.1230E+02\tg\t2.8671E+03\t2.3548E+03\t5.5966E+00\t5.1230E+02\tall\tGadiculus argenteus\tGadiculus\tectotherm vertebrate\t7.7720E+00\tcm\tL = 10^ ((logM-log(0.0058))/3.1083)\t2\tFroese & Pauly (2007)\t7.7720E+00\tmass\tn/a\tn/a\tindividual\t3.4000E+00\tg\t2.4569E+01\t2.1169E+01\t7.2261E+00\t3.4000E+00\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34929\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t8.8300E+01\tmm\ttotal length\t7.2406E+01\t0.0000E+00\t8.8300E+01\tFishbase (species)\t8.8300E+00\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t7.3261E+00\tg\t3.6030E+01\t2.8704E+01\t4.9180E+00\t7.3261E+00\tall\tGonostomatidae sp.\tBristlemouth\tectotherm vertebrate\t5.4092E+00\tcm\tL = 10^ ((logM-log(0.0047))/2.964)\t3\tFroese & Pauly (2007)\t5.4092E+00\tmass\tn/a\tn/a\tindividual\t7.0000E-01\tg\t8.2827E+00\t7.5827E+00\t1.1832E+01\t7.0000E-01\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34930\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t8.8300E+01\tmm\ttotal length\t7.2406E+01\t0.0000E+00\t8.8300E+01\tFishbase (species)\t8.8300E+00\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t7.3261E+00\tg\t3.6030E+01\t2.8704E+01\t4.9180E+00\t7.3261E+00\tall\tGonostomatidae sp.\tBristlemouth\tectotherm vertebrate\t5.4092E+00\tcm\tL = 10^ ((logM-log(0.0047))/2.964)\t3\tFroese & Pauly (2007)\t5.4092E+00\tmass\tn/a\tn/a\tindividual\t7.0000E-01\tg\t8.2827E+00\t7.5827E+00\t1.1832E+01\t7.0000E-01\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n" + "34931\tn/a\tn/a\tZeus faber\tJohn dory\tectotherm vertebrate\tadult\tpiscivorous\t3.5470E+02\tmm\ttotal length\t2.9085E+02\t0.0000E+00\t3.5470E+02\tFishbase (species)\t3.5470E+01\tmid-class\tM=0.0230SL^2.9114\tDorel (1986)\t1\t4.1983E+02\tg\t2.3354E+03\t1.9156E+03\t5.5628E+00\t4.1983E+02\tall\tMicromesistius potassou\tBlue-whiting\tectotherm vertebrate\t2.1704E+01\tcm\tL = 10^ ((logM-log(0.0038))/3.082)\t1\tDorel (1986)\t2.1704E+01\tmass\tn/a\tn/a\tindividual\t5.0000E+01\tg\t5.3502E+02\t4.8502E+02\t1.0700E+01\t5.0000E+01\tWeighed\tn/a\t0\tEastern Mediterranean\t38�00'N\t23�00'E\t75\t19.3\t4.6\t435\t17\tStergiou & Fourtouni 1991\tEuboikos and Pagassitikos Gulfs\tPredator length mid-class\n";
    TestParserFactory parserFactory = new TestParserFactory(new HashMap<String, String>() {

        {
            put(StudyImporterForBarnes.RESOURCE_PATH, firstFourLines);
            put(StudyImporterForBarnes.REFERENCE_PATH, "short,full\nBethea et al (2004),something long\nStergiou & Fourtouni 1991,something longer");
        }
    });
    StudyImporterForBarnes importer = new StudyImporterForBarnes(parserFactory, nodeFactory);
    importStudy(importer);
    Taxon taxon = taxonIndex.findTaxonByName("Zeus faber");
    Iterable<Relationship> relationships = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    for (Relationship relationship : relationships) {
        Node predatorSpecimenNode = relationship.getStartNode();
        assertThat((String) predatorSpecimenNode.getProperty(SpecimenConstant.LIFE_STAGE_LABEL), is("post-juvenile adult stage"));
        assertThat((String) predatorSpecimenNode.getProperty(SpecimenConstant.LIFE_STAGE_ID), is("UBERON:0000113"));
    }
    assertThat(taxon, is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Rhizoprionodon terraenovae"), is(notNullValue()));
    assertThat("missing location", nodeFactory.findLocation(new LocationImpl(38.0, 23.0, -75.0, null)), is(notNullValue()));
}

Example 15 with LocationImpl

use of org.eol.globi.domain.LocationImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForCookTest method importFirstFewLines.

@Test
public void importFirstFewLines() throws IOException, NodeFactoryException, StudyImporterException {
    String firstFiveLines = "\"Date\",\"Individual\",\"Fish Length\",\"Infected\",\"Iso 1\",\"Iso 2\",\"Iso 3\",\"Iso 4 \",\"Iso 5\",\"Iso #\",,\n" + "8/10/2010,22,15.6,1,\"NA\",\"NA\",0,0,0,2,,\"Notes: All fish collected were Atlantic Croaker (Micropogonias undulatus) and measured in total length (cm). Isopods collected were Cymothoa excisa. For the Infected column 1= infected and 0= not infected. Numbers for the isopods are total length in cm and the Iso# represents the number of isopods found per fish. \"\n" + "8/10/2010,1,14.7,1,1.6,0.67,0,0,0,2,,\n" + "8/10/2010,5,14.2,1,1.53,0.7,0,0,0,2,,\n" + "8/10/2010,2,13.2,1,1.42,0.71,0.52,0.45,0,4,,\n";
    StudyImporterForCook importer = new StudyImporterForCook(new TestParserFactory(firstFiveLines), nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    Taxon hostTaxon = taxonIndex.findTaxonByName("Micropogonias undulatus");
    assertThat(hostTaxon, is(notNullValue()));
    Taxon parasiteTaxon = taxonIndex.findTaxonByName("Cymothoa excisa");
    assertThat(parasiteTaxon, is(notNullValue()));
    assertThat("missing location", nodeFactory.findLocation(new LocationImpl(27.85, -(97.0 + 8.0 / 60.0), -3.0, null)), is(notNullValue()));
    int count = 0;
    boolean foundFirstHost = false;
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(study);
    for (Relationship collected_rel : specimens) {
        assertThat(collected_rel.getProperty(SpecimenConstant.DATE_IN_UNIX_EPOCH), is(notNullValue()));
        Node specimen = collected_rel.getEndNode();
        if (specimen.hasProperty(SpecimenConstant.LENGTH_IN_MM)) {
            Object property = specimen.getProperty(SpecimenConstant.LENGTH_IN_MM);
            if (new Double(156.0).equals(property)) {
                assertTaxonClassification(specimen, ((NodeBacked) hostTaxon).getUnderlyingNode());
                foundFirstHost = true;
                Iterable<Relationship> parasiteRel = specimen.getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(InteractType.PARASITE_OF));
                for (Relationship relationship : parasiteRel) {
                    Node parasite = relationship.getStartNode();
                    assertThat(parasite.hasProperty(SpecimenConstant.LENGTH_IN_MM), is(false));
                    assertTaxonClassification(parasite, ((NodeBacked) parasiteTaxon).getUnderlyingNode());
                }
            }
        }
        count++;
    }
    assertThat(count, is(14));
    assertThat(foundFirstHost, is(true));
}