Examples with InteractionListener org.eol.globi.process.InteractionListener used on opensource projects

Example 16 with InteractionListener

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

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDirUnsupportedDescriptionType.

@Test
public void importTaxonDescriptionsFromDirUnsupportedDescriptionType() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer-unsupported-description-type/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size(), is(0));
}

Example 17 with InteractionListener

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

the class DatasetImporterForDwCATest method importRecordsFromZip.

@Test
public void importRecordsFromZip() throws StudyImporterException, IOException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/dwca.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("file:///some/path/data.zip"), inStream -> inStream);
    JsonNode jsonNode = new ObjectMapper().readTree("{ " + "\"interactionTypeId\": \"http://purl.obolibrary.org/obo/RO_0002437\"," + "\"url\": \"" + resource.toExternalForm() + "\"" + "}");
    dataset.setConfig(jsonNode);
    studyImporterForDwCA.setDataset(dataset);
    String expectedCitation = dataset.getCitation();
    AtomicBoolean someRecords = new AtomicBoolean(false);
    Set<String> resourceTypes = new TreeSet<>();
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            String associatedTaxa = interaction.get("http://rs.tdwg.org/dwc/terms/associatedTaxa");
            String dynamicProperties = interaction.get("http://rs.tdwg.org/dwc/terms/dynamicProperties");
            assertThat(StringUtils.isNotBlank(associatedTaxa) || StringUtils.isNotBlank(dynamicProperties), is(true));
            assertThat(interaction.get(SOURCE_TAXON_NAME), is(not(nullValue())));
            assertThat(interaction.get(TaxonUtil.TARGET_TAXON_NAME), is(not(nullValue())));
            assertThat(interaction.get(INTERACTION_TYPE_NAME), is(not(nullValue())));
            assertThat(interaction.get(DatasetImporterForTSV.DATASET_CITATION), containsString(expectedCitation));
            assertThat(interaction.get(REFERENCE_ID), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            assertThat(interaction.get(REFERENCE_URL), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            resourceTypes.addAll(Arrays.asList(splitByPipes(interaction.get(RESOURCE_TYPES))));
            someRecords.set(true);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(someRecords.get(), is(true));
    assertThat(resourceTypes, containsInAnyOrder("http://rs.tdwg.org/dwc/terms/dynamicProperties", "http://rs.tdwg.org/dwc/terms/Occurrence", "http://rs.tdwg.org/dwc/terms/associatedTaxa"));
}

Example 18 with InteractionListener

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

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDir.

@Test
public void importTaxonDescriptionsFromDir() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size() > 0, is(true));
    assertThat(links.get(0).get(DATASET_CITATION), containsString("org/globalbioticinteractions/dataset/coetzer/"));
    assertThat(links.get(0).get(REFERENCE_CITATION), is("Cockerell, T.D.A. 1937. African bees of the genera Ceratina, Halictus and Megachile. 254 pp. William Clowes and Sons, London"));
    assertThat(links.get(0).get(TARGET_TAXON_NAME), is("Chaetodactylus leleupi"));
    assertThat(links.get(0).get(SOURCE_TAXON_NAME), is("Ceratina ruwenzorica Cockerell, 1937"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is("Parasite"));
    assertThat(links.get(0).get(RESOURCE_TYPES), is("http://rs.gbif.org/terms/1.0/Reference"));
}

Example 19 with InteractionListener

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

the class DatasetImporterForDwCATest method hasResourceRelationshipsOccurrenceToOccurrenceRemarks.

@Test
public void hasResourceRelationshipsOccurrenceToOccurrenceRemarks() throws IOException, URISyntaxException {
    URI sampleArchive = getClass().getResource("fmnh-rr-remarks-test.zip").toURI();
    Archive archive = DwCAUtil.archiveFor(sampleArchive, "target/tmp");
    AtomicInteger numberOfFoundLinks = new AtomicInteger(0);
    importResourceRelationshipExtension(archive, new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            numberOfFoundLinks.incrementAndGet();
            if (1 == numberOfFoundLinks.get()) {
                assertThat(interaction.get(SOURCE_TAXON_NAME), is("Trichobius parasparsus Wenzel, 1976"));
                assertThat(interaction.get(SOURCE_OCCURRENCE_ID), is("8afec7db-7b19-44f7-8ac8-8d98614e71d2"));
                assertThat(interaction.get(INTERACTION_TYPE_NAME), is("Ectoparasite of"));
                assertThat(interaction.get(INTERACTION_TYPE_ID), is(nullValue()));
                assertThat(interaction.get(DatasetImporterForTSV.BASIS_OF_RECORD_NAME), is("PreservedSpecimen"));
                assertThat(interaction.get(TaxonUtil.TARGET_TAXON_NAME), is("Donald duckus"));
                assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), is("A. L. Tuttle | M. D. Tuttle"));
            }
            assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), is(notNullValue()));
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
        }
    });
    assertThat(numberOfFoundLinks.get(), is(1));
}

Example 20 with InteractionListener

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

the class DatasetImporterForDwCATest method importRecordsFromArctosArchive.

@Test
public void importRecordsFromArctosArchive() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/arctos_mvz_bird_small.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream));
    List<String> families = new ArrayList<>();
    AtomicBoolean someRecords = new AtomicBoolean(false);
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(REFERENCE_URL), startsWith("http://arctos.database.museum/guid/"));
            assertThat(interaction.get(SOURCE_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Bird:180448?seid=587053"), is("http://arctos.database.museum/guid/MVZ:Bird:183644?seid=158590"), is("http://arctos.database.museum/guid/MVZ:Bird:58090?seid=657121")));
            if (interaction.containsKey(DatasetImporterForTSV.TARGET_OCCURRENCE_ID)) {
                assertThat(interaction.get(DatasetImporterForTSV.TARGET_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Herp:241200"), is("http://arctos.database.museum/guid/MVZ:Bird:183643"), is("http://arctos.database.museum/guid/MVZ:Bird:58093")));
            }
            assertThat(interaction.get(SOURCE_TAXON_FAMILY), anyOf(is("Accipitridae"), is("Strigidae")));
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/associatedOccurrences | http://rs.tdwg.org/dwc/terms/Occurrence"));
            someRecords.set(true);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(someRecords.get(), is(true));
}