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Example 1 with StudyImporterForGitHubData

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

the class Normalizer method importData.

void importData(GraphDatabaseService graphService, String cacheDir) {
    NodeFactoryNeo4j factory = new NodeFactoryNeo4j(graphService);
    factory.setEcoregionFinder(getEcoregionFinder());
    factory.setDoiResolver(new DOIResolverImpl());
    try {
        CacheFactory cacheFactory = dataset -> new CacheLocalReadonly(dataset.getNamespace(), cacheDir);
        DatasetFinder finder = new DatasetFinderLocal(cacheDir, cacheFactory);
        StudyImporter importer = new StudyImporterForGitHubData(new ParserFactoryLocal(), factory, finder);
        importer.setDataset(new DatasetLocal());
        importer.setLogger(new StudyImportLogger());
        importer.importStudy();
    } catch (StudyImporterException e) {
        LOG.error("problem encountered while importing [" + StudyImporterForGitHubData.class.getName() + "]", e);
    }
    EcoregionFinder regionFinder = getEcoregionFinder();
    if (regionFinder != null) {
        regionFinder.shutdown();
    }
}
Also used : OpenTreeTaxonIndex(org.eol.globi.opentree.OpenTreeTaxonIndex) NonResolvingTaxonIndex(org.eol.globi.taxon.NonResolvingTaxonIndex) EcoregionFinder(org.eol.globi.geo.EcoregionFinder) DatasetFinderLocal(org.globalbioticinteractions.dataset.DatasetFinderLocal) URISyntaxException(java.net.URISyntaxException) Options(org.apache.commons.cli.Options) TaxonCacheService(org.eol.globi.taxon.TaxonCacheService) DOIResolverCache(org.eol.globi.service.DOIResolverCache) ResolvingTaxonIndex(org.eol.globi.taxon.ResolvingTaxonIndex) HelpFormatter(org.apache.commons.cli.HelpFormatter) StringUtils(org.apache.commons.lang3.StringUtils) ArrayList(java.util.ArrayList) StudyImporterException(org.eol.globi.data.StudyImporterException) EcoregionFinderProxy(org.eol.globi.service.EcoregionFinderProxy) ParserFactoryLocal(org.eol.globi.data.ParserFactoryLocal) GraphDatabaseService(org.neo4j.graphdb.GraphDatabaseService) BasicParser(org.apache.commons.cli.BasicParser) CommandLine(org.apache.commons.cli.CommandLine) GraphService(org.eol.globi.db.GraphService) URI(java.net.URI) EcoregionFinderFactoryImpl(org.eol.globi.geo.EcoregionFinderFactoryImpl) HttpUtil(org.eol.globi.util.HttpUtil) Option(org.apache.commons.cli.Option) Taxon(org.eol.globi.domain.Taxon) CommandLineParser(org.apache.commons.cli.CommandLineParser) MalformedURLException(java.net.MalformedURLException) CacheLocalReadonly(org.globalbioticinteractions.cache.CacheLocalReadonly) DatasetFinder(org.eol.globi.service.DatasetFinder) DatasetLocal(org.eol.globi.service.DatasetLocal) StudyImporterForGitHubData(org.eol.globi.data.StudyImporterForGitHubData) DOIResolverImpl(org.eol.globi.service.DOIResolverImpl) NodeFactoryNeo4j(org.eol.globi.data.NodeFactoryNeo4j) List(java.util.List) StudyImporter(org.eol.globi.data.StudyImporter) ParseException(org.apache.commons.cli.ParseException) GraphExporterImpl(org.eol.globi.export.GraphExporterImpl) Version(org.eol.globi.Version) Log(org.apache.commons.logging.Log) LogFactory(org.apache.commons.logging.LogFactory) CacheFactory(org.globalbioticinteractions.cache.CacheFactory) EcoregionFinder(org.eol.globi.geo.EcoregionFinder) StudyImporterForGitHubData(org.eol.globi.data.StudyImporterForGitHubData) DOIResolverImpl(org.eol.globi.service.DOIResolverImpl) NodeFactoryNeo4j(org.eol.globi.data.NodeFactoryNeo4j) DatasetLocal(org.eol.globi.service.DatasetLocal) StudyImporter(org.eol.globi.data.StudyImporter) CacheLocalReadonly(org.globalbioticinteractions.cache.CacheLocalReadonly) StudyImporterException(org.eol.globi.data.StudyImporterException) DatasetFinder(org.eol.globi.service.DatasetFinder) CacheFactory(org.globalbioticinteractions.cache.CacheFactory) DatasetFinderLocal(org.globalbioticinteractions.dataset.DatasetFinderLocal) ParserFactoryLocal(org.eol.globi.data.ParserFactoryLocal)

Aggregations

MalformedURLException (java.net.MalformedURLException)1 URI (java.net.URI)1 URISyntaxException (java.net.URISyntaxException)1 ArrayList (java.util.ArrayList)1 List (java.util.List)1 BasicParser (org.apache.commons.cli.BasicParser)1 CommandLine (org.apache.commons.cli.CommandLine)1 CommandLineParser (org.apache.commons.cli.CommandLineParser)1 HelpFormatter (org.apache.commons.cli.HelpFormatter)1 Option (org.apache.commons.cli.Option)1 Options (org.apache.commons.cli.Options)1 ParseException (org.apache.commons.cli.ParseException)1 StringUtils (org.apache.commons.lang3.StringUtils)1 Log (org.apache.commons.logging.Log)1 LogFactory (org.apache.commons.logging.LogFactory)1 Version (org.eol.globi.Version)1 NodeFactoryNeo4j (org.eol.globi.data.NodeFactoryNeo4j)1 ParserFactoryLocal (org.eol.globi.data.ParserFactoryLocal)1 StudyImporter (org.eol.globi.data.StudyImporter)1 StudyImporterException (org.eol.globi.data.StudyImporterException)1