use of org.eol.globi.domain.Location in project eol-globi-data by jhpoelen.
the class StudyImporterForSzoboszlaiIT method importAll.
@Test
public void importAll() throws StudyImporterException, IOException {
JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Szoboszlai AI, Thayer JA, Wood SA, Sydeman WJ, Koehn LE (2015) Data from: Forage species in predator diets: synthesis of data from the California Current. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + " \"doi\": \"http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + " \"format\": \"szoboszlai\",\n" + " \"resources\": {\n" + " \"links\": \"http://datadryad.org/bitstream/handle/10255/dryad.94536/CCPDDlinkdata_v1.csv\",\n" + " \"shapes\": \"http://datadryad.org/bitstream/handle/10255/dryad.94535/CCPDDlocationdata_v1.zip\"\n" + " }\n" + "}");
DatasetImpl dataset = new DatasetImpl("someRepo", URI.create("http://example.com"));
dataset.setConfig(config);
ParserFactory parserFactory = new ParserFactoryForDataset(dataset);
StudyImporterForSzoboszlai importer = new StudyImporterForSzoboszlai(parserFactory, nodeFactory);
importer.setDataset(dataset);
importStudy(importer);
List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
assertThat(allStudies.size(), is(not(0)));
Study firstStudy = allStudies.get(0);
Iterable<Relationship> specimens = NodeUtil.getSpecimens(firstStudy);
for (Relationship specimen : specimens) {
Specimen specimenNode = new SpecimenNode(specimen.getEndNode());
Location sampleLocation = specimenNode.getSampleLocation();
assertThat(sampleLocation, is(notNullValue()));
assertThat(sampleLocation.getLatitude(), is(notNullValue()));
assertThat(sampleLocation.getLongitude(), is(notNullValue()));
}
assertThat(taxonIndex.findTaxonByName("Thunnus thynnus"), is(notNullValue()));
assertThat(nodeFactory.findLocation(new LocationImpl(34.00824202376044, -120.72716166720323, null, null)), is(notNullValue()));
}
use of org.eol.globi.domain.Location in project eol-globi-data by jhpoelen.
the class StudyImporterForBrose method addInteractionForConsumer.
private void addInteractionForConsumer(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
Location location = null;
String locationString = parser.getValueByLabel("Geographic location");
LatLng latLng = LOC_MAP.get(StringUtils.trim(locationString));
if (latLng == null) {
getLogger().warn(localStudy, "failed to find location for [" + locationString + "]");
} else {
location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
String habitat = StringUtils.join(parser.getValueByLabel("General habitat"), " ", parser.getValueByLabel("Specific habitat"));
String habitatId = "BROSE:" + habitat.replaceAll("\\W", "_");
nodeFactory.getOrCreateEnvironments(location, habitatId, habitat);
}
Specimen consumer = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
consumer.caughtIn(location);
addLifeStage(parser, consumer, "Lifestage consumer");
String name = getName(parser, "Taxonomy resource", "Common name(s) resource");
if (StringUtils.isBlank(name) || StringUtils.length(name) < 2) {
String message = "found (near) empty prey name on line [" + parser.lastLineNumber() + "] + [" + name + "]";
LOG.warn(message);
getLogger().warn(localStudy, message);
} else {
Specimen resource = nodeFactory.createSpecimen(localStudy, new TaxonImpl(name, null));
resource.caughtIn(location);
addLifeStage(parser, resource, "Lifestage - resource");
String interactionType = parser.getValueByLabel("Type of feeding interaction");
Map<String, InteractType> typeMapping = new HashMap<String, InteractType>() {
{
put("predacious", InteractType.PREYS_UPON);
put("predator", InteractType.PREYS_UPON);
put("herbivorous", InteractType.ATE);
put("parasitoid", InteractType.PARASITE_OF);
put("parasitic", InteractType.PARASITE_OF);
put("bacterivorous", InteractType.ATE);
put("omnivore", InteractType.ATE);
put("detritivorous", InteractType.ATE);
put("pathogen", InteractType.PATHOGEN_OF);
}
};
InteractType interactType = typeMapping.get(interactionType);
if (interactType == null) {
throw new StudyImporterException("found unsupported interaction type [" + interactionType + "]");
}
consumer.interactsWith(resource, interactType);
}
}
use of org.eol.globi.domain.Location in project eol-globi-data by jhpoelen.
the class StudyImporterForBaremore method importStudy.
@Override
public void importStudy() throws StudyImporterException {
Study study;
try {
LabeledCSVParser parser = parserFactory.createParser(DATA_SOURCE, CharsetConstant.UTF8);
String[] line;
study = nodeFactory.getOrCreateStudy(new StudyImpl("Baremore 2010", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, "doi:10.3354/ab00214", ExternalIdUtil.toCitation("Ivy E. Baremore", "Prey Selection By The Atlantic Angel Shark Squatina Dumeril In The Northeastern Gulf Of Mexico.", "2010")));
Location collectionLocation = nodeFactory.getOrCreateLocation(new LocationImpl(29.219302, -87.06665, null, null));
Map<Integer, Specimen> specimenMap = new HashMap<Integer, Specimen>();
while ((line = parser.getLine()) != null) {
Integer sharkId = Integer.parseInt(line[0]);
String collectionDateString = line[1];
if (isBlank(collectionDateString)) {
getLogger().warn(study, "line [" + parser.getLastLineNumber() + "] in [" + DATA_SOURCE + "]: missing collection date");
} else {
Specimen predatorSpecimen = specimenMap.get(sharkId);
if (predatorSpecimen == null) {
predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Squatina dumeril", null));
predatorSpecimen.caughtIn(collectionLocation);
addLifeStage(parser, predatorSpecimen);
addCollectionDate(collectionDateString, predatorSpecimen);
}
specimenMap.put(sharkId, predatorSpecimen);
String totalLengthInCm = line[3];
try {
Double lengthInMm = Double.parseDouble(totalLengthInCm) * 10.0;
predatorSpecimen.setLengthInMm(lengthInMm);
} catch (NumberFormatException ex) {
throw new StudyImporterException("failed to parse length [" + totalLengthInCm);
}
String preySpeciesDescription = line[7];
if (StringUtils.isBlank(preySpeciesDescription)) {
getLogger().info(study, "found blank prey species description [" + preySpeciesDescription + "] on line [" + parser.lastLineNumber() + "]");
} else {
Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preySpeciesDescription, null));
preySpecimen.caughtIn(collectionLocation);
predatorSpecimen.ate(preySpecimen);
nodeFactory.setUnixEpochProperty(preySpecimen, nodeFactory.getUnixEpochProperty(predatorSpecimen));
}
}
}
} catch (IOException e) {
throw new StudyImporterException("failed to parse labels", e);
}
}
use of org.eol.globi.domain.Location in project eol-globi-data by jhpoelen.
the class StudyImporterForBlewett method buildLocationTimeMaps.
private void buildLocationTimeMaps(Map<String, Location> collectionLocationMap, Map<String, Date> collectionTimeMap, Study study) throws IOException, StudyImporterException {
LabeledCSVParser locationParser = parserFactory.createParser("blewett/SnookDietData2000_02_Charlotte_Harbor_FL_Blewett_date_and_abiotic.csv", CharsetConstant.UTF8);
String[] line;
while ((line = locationParser.getLine()) != null) {
if (line.length < 3) {
getLogger().warn(study, "line:" + locationParser.getLastLineNumber() + " [" + StringUtils.join(line, ",") + "] has missing location information");
}
String collectionCode = locationParser.getValueByLabel(COLLECTION_NO);
if (StringUtils.isBlank(collectionCode)) {
getLogger().warn(study, "blank location code for line: [" + locationParser.getLastLineNumber() + "]");
}
String latitude = locationParser.getValueByLabel("Latitude");
if (StringUtils.isBlank(latitude)) {
getLogger().warn(study, "blank value for lattitude for line: [" + locationParser.getLastLineNumber() + "]");
}
String longitude = locationParser.getValueByLabel("Longitude");
if (StringUtils.isBlank(longitude)) {
getLogger().warn(study, "blank value for longitude for line: [" + locationParser.getLastLineNumber() + "]");
}
Location location;
try {
location = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), 0.0, null));
} catch (NodeFactoryException e) {
throw new StudyImporterException("failed to create location", e);
}
collectionLocationMap.put(collectionCode, location);
String timeString = locationParser.getValueByLabel("Time");
if (StringUtils.isBlank(timeString)) {
getLogger().warn(study, "blank value for time for line: [" + locationParser.getLastLineNumber() + "]");
}
String dateString = locationParser.getValueByLabel("Date");
if (StringUtils.isBlank(dateString)) {
getLogger().warn(study, "blank value for date for line: [" + locationParser.getLastLineNumber() + "]");
}
String dateTimeString = dateString + " " + timeString;
try {
Date dateTime = parseDateString(dateTimeString);
collectionTimeMap.put(collectionCode, dateTime);
} catch (ParseException e) {
throw new StudyImporterException("failed to parse date time [" + dateTimeString + "] for collection [" + collectionCode + "] on line [" + locationParser.getLastLineNumber() + "]");
}
}
}
use of org.eol.globi.domain.Location in project eol-globi-data by jhpoelen.
the class StudyImporterForBarnes method addInteractionForPredator.
private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
addLifeStage(parser, predator);
Double latitude = LocationUtil.parseDegrees(parser.getValueByLabel("Latitude"));
Double longitude = LocationUtil.parseDegrees(parser.getValueByLabel("Longitude"));
String depth = parser.getValueByLabel("Depth");
Double altitudeInMeters = -1.0 * Double.parseDouble(depth);
Location location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, altitudeInMeters, null));
predator.caughtIn(location);
String preyName = parser.getValueByLabel("Prey");
if (StringUtils.isBlank(preyName)) {
getLogger().warn(localStudy, "found empty prey name on line [" + parser.lastLineNumber() + "]");
} else {
Specimen prey = nodeFactory.createSpecimen(localStudy, new TaxonImpl(preyName, null));
prey.caughtIn(location);
predator.ate(prey);
}
}
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