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

Example 16 with Location

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

the class StudyImporterForBell method getLocation.

protected Location getLocation(LabeledCSVParser parser, Specimen parasite) throws NodeFactoryException {
    String latitude = parser.getValueByLabel("DEC_LAT");
    String longitude = parser.getValueByLabel("DEC_LONG");
    Location location = null;
    if (StringUtils.isNotBlank(latitude) && StringUtils.isNotBlank(longitude)) {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), null, null));
    }
    return location;
}

Example 17 with Location

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

the class StudyImporterForBell method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    for (String resource : RESOURCE) {
        LabeledCSVParser parser = null;
        try {
            parser = parserFactory.createParser(resource, "UTF-8");
            while (parser.getLine() != null) {
                String sourceCitation = "Bell, K. C., Matek, D., Demboski, J. R., & Cook, J. A. (2015). Expanded Host Range of Sucking Lice and Pinworms of Western North American Chipmunks. Comparative Parasitology, 82(2), 312–321. doi:10.1654/4756.1 . Data provided by Kayce C. Bell.";
                String guid = parser.getValueByLabel("GUID");
                String externalId = "http://arctos.database.museum/guid/" + guid;
                String description = null;
                String collectionId = null;
                for (String key : REFS.keySet()) {
                    if (guid.startsWith(key)) {
                        description = REFS.get(key);
                        collectionId = key;
                        break;
                    }
                }
                if (StringUtils.isBlank(description)) {
                    LOG.warn("missing collectionId [" + guid + "] in file [" + resource + "] on line [" + parser.lastLineNumber() + "]");
                    description = sourceCitation;
                    collectionId = "";
                }
                Study study = nodeFactory.getOrCreateStudy(new StudyImpl("bell-" + collectionId, sourceCitation, "http://dx.doi.org/10.1654/4756.1", ExternalIdUtil.toCitation(null, sourceCitation + " " + description, null)));
                String genus = parser.getValueByLabel("Genus");
                String species = parser.getValueByLabel("Species");
                String parasiteName = StringUtils.join(new String[] { StringUtils.trim(genus), StringUtils.trim(species) }, " ");
                Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                parasite.setExternalId(externalId);
                Location location = getLocation(parser, parasite);
                parasite.caughtIn(location);
                String scientificName = parser.getValueByLabel("SCIENTIFIC_NAME");
                String hostName = StringUtils.trim(scientificName);
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                host.caughtIn(location);
                host.setExternalId(externalId);
                parasite.interactsWith(host, InteractType.PARASITE_OF);
                Date date = parseDate(parser);
                nodeFactory.setUnixEpochProperty(parasite, date);
                nodeFactory.setUnixEpochProperty(host, date);
            }
        } catch (Throwable e) {
            throw new StudyImporterException(getErrorMessage(resource, parser), e);
        }
    }
}

Example 18 with Location

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

the class StudyImporterForBlewett method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String citation = "Blewett DA, Hensley RA, and Stevens PW, Feeding Habits of Common Snook, Centropomus Undecimalis, in Charlotte Harbor, Florida, Gulf and Caribbean Research Vol 18, 1–13, 2006. doi:10.18785/gcr.1801.01 ";
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Blewett 2006", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, citation));
    try {
        Map<String, Location> collectionLocationMap = new HashMap<>();
        Map<String, Date> collectionTimeMap = new HashMap<String, Date>();
        buildLocationTimeMaps(collectionLocationMap, collectionTimeMap, study);
        parsePredatorPreyInteraction(study, collectionLocationMap, collectionTimeMap);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create taxon", e);
    } catch (TermLookupServiceException e) {
        throw new StudyImporterException("failed to map terms", e);
    }
}

Example 19 with Location

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

the class StudyImporterForBlewett method setLocationAndDate.

private void setLocationAndDate(Map<String, Location> locationMap, Map<String, Date> collectionTimeMap, List<Specimen> items, String collectionCode) throws NodeFactoryException {
    String collectionCodeTrim = collectionCode.trim();
    Location location = locationMap.get(collectionCodeTrim);
    if (location != null) {
        for (Specimen item : items) {
            item.caughtIn(location);
        }
    }
    Date collectionDatetime = collectionTimeMap.get(collectionCodeTrim);
    if (collectionDatetime != null) {
        for (Specimen item : items) {
            nodeFactory.setUnixEpochProperty(item, collectionDatetime);
        }
    }
}

Example 20 with Location

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

the class StudyImporterForGoMexSI2Test method parseLocation.

@Test
public void parseLocation() throws IOException, StudyImporterException {
    final String locationLines = "DATA_ID,PRED_ID,LOC_ID,LME_CODE,COUNTRY,STATE,GULF_OCTANT,LOCALE_NAME,LOCALE_TYPE,BAY_HIERARC_LEVEL,SAMP_DEP_REALM,LOC_CENTR_LAT,LOC_CENTR_LONG,LOC_POLY_COORDS,PRED_POLY_SHAPEFILE_ID,PRED_CENT_SHAPEFILE_ID,PRED_STAT_SHAPEFILE_ID,LOC_POLY_SOURCE,LOC_POLY_CONF,MAJOR_LOC_NAME,MAJOR_LOC_TYPE,MIN_DEP_LOC,MAX_DEP_LOC,MN_DEP_LOC,MIN_DEP_SAMP,MAX_DEP_SAMP,MN_DEP_SAMP,TIME_ZONE,START_YEAR,START_MON,START_DAY,START_TIME,START_SEAS,END_YEAR,END_MON,END_DAY,END_TIME,END_SEAS,REALM,PROVINCE,ECOREGION,HAB_SYSTEM,HAB_SUBSYSTEM,TIDAL_ZONE,SYS_CONF,LOC_NOTES,NUM_SAMPS,ENTRY_DATE,ENTRY_PERSON,EDITED_DATE,DATA_EDITOR,MODIFY_DATE,DATA_MODIFIER\n" + "ACT_16R,Cchr.1,ACT_16r.1,GOM,US,LA,NNW,Louisiana inner continental shelf,Continental shelf,NA,Demersal,29.346953,-92.980614,\"((-92.6729107838999,29.3941413332999),(-92.5604838626999,29.2066775354),(-92.7326173694,29.1150784684999),(-92.9638307704999,29.1171045174),(-93.3169089704999,29.3616452463),(-93.4007435505999,29.5222620776999),(-93.3169089704999,29.6243402981),(-93.1045280342,29.6340566488),(-92.6729107838999,29.3941413332999))\",,,,Inferred from station locations,high,Louisiana continental shelf,Gulf/Ocean waters,9.094,18.188,13.641,9.094,18.188,13.641,CDST,1970,7,NA,0:00,summer,1973,2,NA,0:00,winter,TNA,WTNA,43,Marine,Nearshore,Subtidal,NA,NA,NA,NA,Jim Simons,NA,Jim Simons,15/06/2016,Theresa Mitchell\n" + "ACT_16R,Cchr.1,ACT_16r.2,GOM,US,LA,NNW,Louisiana mid continental shelf,Continental shelf,NA,Demersal,29.032598,-92.287009,\"((-92.1815365767999,29.1068886358999),(-92.200079333,29.0069336331),(-92.3030548952999,28.9075567952),(-92.4770626883999,28.8892759983999),(-92.5999700862,28.9468493538999),(-92.6034249349,29.0088070450999),(-92.5255192441999,29.0774757406),(-92.3918542331,29.148292841),(-92.2231376575,29.1384141105999),(-92.1815365767999,29.1068886358999))\",,,,Inferred from station locations,high,Louisiana continental shelf,Gulf/Ocean waters,18.188,54.564,36.376,18.188,54.564,36.376,CDST,1970,7,NA,0:00,summer,1973,2,NA,0:00,winter,TNA,WTNA,43,Marine,Offshore,Subtidal,NA,NA,NA,NA,Jim Simons,NA,Jim Simons,15/06/2016,Theresa Mitchell\n" + "ACT_16R,Cchr.1,ACT_16r.1,GOM,US,LA,NNW,Louisiana inner continental shelf,Continental shelf,NA,Demersal,29.346953,-92.980614,\"((-92.6729107838999,29.3941413332999),(-92.5604838626999,29.2066775354),(-92.7326173694,29.1150784684999),(-92.9638307704999,29.1171045174),(-93.3169089704999,29.3616452463),(-93.4007435505999,29.5222620776999),(-93.3169089704999,29.6243402981),(-93.1045280342,29.6340566488),(-92.6729107838999,29.3941413332999))\",,,,Inferred from station locations,high,Louisiana continental shelf,Gulf/Ocean waters,9.094,18.188,13.641,9.094,18.188,13.641,CDST,1970,7,NA,0:00,summer,1973,2,NA,0:00,winter,TNA,WTNA,43,Marine,Nearshore,Subtidal,NA,NA,NA,NA,Jim Simons,NA,Jim Simons,15/06/2016,Theresa Mitchell\n" + "ACT_16R,Cchr.1,ACT_16r.2,GOM,US,LA,NNW,Louisiana mid continental shelf,Continental shelf,NA,Demersal,29.032598,-92.287009,\"((-92.1815365767999,29.1068886358999),(-92.200079333,29.0069336331),(-92.3030548952999,28.9075567952),(-92.4770626883999,28.8892759983999),(-92.5999700862,28.9468493538999),(-92.6034249349,29.0088070450999),(-92.5255192441999,29.0774757406),(-92.3918542331,29.148292841),(-92.2231376575,29.1384141105999),(-92.1815365767999,29.1068886358999))\",,,,Inferred from station locations,high,Louisiana continental shelf,Gulf/Ocean waters,18.188,54.564,36.376,18.188,54.564,36.376,CDST,1970,7,NA,0:00,summer,1973,2,NA,0:00,winter,TNA,WTNA,43,Marine,Offshore,Subtidal,NA,NA,NA,NA,Jim Simons,NA,Jim Simons,15/06/2016,Theresa Mitchell\n";
    final LabeledCSVParser parser = new LabeledCSVParser(new CSVParser(IOUtils.toInputStream(locationLines)));
    parser.getLine();
    final Location location = StudyImporterForGoMexSI2.parseLocation("someMickeyMouseresource.csv", parser);
    assertThat(location.getLatitude(), is(29.346953d));
    assertThat(location.getLongitude(), is(-92.980614d));
    assertThat(location.getAltitude(), is(-13.641d));
    assertThat(location.getLocality(), is("Louisiana inner continental shelf"));
    assertThat(location.getFootprintWKT(), is(WKT_FOOTPRINT));
}